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Brainsight User Manual

1. Site eS Set PC x Goto Next Sp Set the Anterior and Posterior Commissures Chapter yy 7 Locate and set the posterior commissure Click Go to Next Step Drag the bounding box limits to fit the edges of the brain in each view If the head appears tilted in the coronal view either due to the scan or the setting of the anterior and posterior commisures use the Alignment bar to rectify the tilt See Figure 7 17 Figure 7 17 Tiik MGE Alignment E Plais abgr the Brigherau Cure brain wiih the Teram bounding box and tie this bom t fie he brains ex benti Lat Loo 4 Goto Previous Step Goto Next Step Set the bounding box 7 Click Go to Next Step If the overlay of the Talairach template the Task Assistant shows you is slightly off click Go to Previous Step either once or twice and reset the AC PC and bounding boxes until you obtain the desired overlay See Figure 7 18 for an example of the overlay 58 Brainsight 1 7 _ SSeS ae Figure 7 18 Note that as in any linear registration between E 2 objects that differ in the way an individual s steps head may differ from the MNI Talairach tem io plate the registration will never be perfect It Is up to the investigator to determine if the registration obtained here is sufficient for their application Tate Aticlint a Verify thak the MHI lt A Talalrach template overlays v ll on the brain Mote that some Innadu
2. to create that day s session prior to modifying any data Start each session in this manner by loading the original template project Register Subject to Images First comfortably position the subject as you normally would Hold the pointer steady as you register the landmarks For this reason you should have an assistant interact with Brainsight while you register the subject USING THE REGISTRATION TASK ASSISTANT There is a registration Task Assistant to guide you through the registration process All interactions are centralized into a single window To start the registration process follow these steps 1 Select the Cursor tool 2 Select New Assisted Reg from the pop up menu at the bottom of the Cursor tool control pane Figure 6 1 ap pears Figure 6 1 O Task Assisbant Step 1 Read Information This step is needed for Brainsight to calculate the relationshie between the subject and tha mage data Before proceeding you will need to h ve cone or do mow the following 1 Load the Subjects anatomical MR or CT data 2 Identify and saree anatoenical kindmarks d markers 3 Save the Information as Braingight Project fle 4 Retrieve the project 50 that the M images and markers are being dismayed 5 Make sure the Polaris Camera is connmectd to the computer and turned on Note that you may n ad to alka 20 about minutes for ihe camera ta warm up Step Infa Go to Previous Step
3. allen key In both cases you will have to loosen the bolts to create space for the T nut to fit into the slot Before as sembling a joint loosen all the associated bolts as much as possible without having the T nut actually come off the bolt and slide the T nut into the slot Find the main horizontal and main vertical bars and the front foot Loosen the butt joint bolts on the end of the horizontal bar so that the T nuts slide into the front slots of the vertical bar Adjust the location of the joint using the length of the vertical portion of the front foot as a guide about 7 from the bottom Tighten the 4 bolts of the butt joint to secure the joint Double check the 4 bolts Take care to ensure that the threaded end of the vertical Chapter 10 93 Est bar is on top If needed adjust the location of the chin rest slider on the vertical bar by loosening the 4 bolts securing it to the bar and sliding it up or down the bar and finally tightening the bolt again Figure 10 15 Figure 10 15 Horizontal and vertical bars Figure 10 15 4 Loosen the bolts of the butt joint for the front foot Figure 10 15A Hold the assembly from the previous step up and insert the front foot into the end of the horizontal bar and tighten the butt joint screws 5 Locate the rear foot Figure 10 15B Loosen the 8 nuts inside the 2 corner brackets to loosen the T nuts Lift the rear part of the assembly and lower the vertical bar onto t
4. zoom camera 51 control 49 Feedback t Rogue Research we are interested in your experience in using the Brainsight TMS version 1 7 User Manual Please take the time to fill out the following survey and mail it to us at the address on the back cover Alternatively if you are viewing the document with a PDF viewer you may paste the body of this survey into an e mail complete it and send it to info rogue re search com This information will be used in our documentation planning activities to improve our products and service Most questions are based on a scale of 1 to 5 where you feel 1 Very dissatisfied 2 Dissatisfied 3 Neutral 4 Satisfied 5 Very satisfied In the Comments region indicate which parts of the document most resemble the problems you had or kinds of structure or information quality you are looking for Append any notes you have to contribute Survey questions I found the technical accuracy of this document to be l 2 3 4 5 Comments I found the technical depth of this document to be l 2 3 4 5 Comments I found the accessibility of this document to be l 2 3 4 5 Comments 102 Brainsight 1 7 l I found the thoroughness of this document to be l 2 3 4 5 Comments I found the brevity or length circle one of this document to be l 2 3 4 5 Comments I found the Plain English or translation of this document to be l 2 3 4 5 Comments I found the explanation of concepts i
5. Chapter N Figure 7 15 Using Electrode Recording l Place the subject tracker using the tracker glasses on og D O Flectrode Recording for LOCATOR the subject being careful not to disturb the EEG elec Pointer Mouse H trodes Subject Name 2 In Brainsight open the Polaris window and set the track ee er status to ON Ensure that the Polaris is configured to ek mb dn ee track the pointer and subject This should be automatic ee eee 3 Open the Electrode Recording window by selecting Windows gt Electrode Recording The window in Figure 7 14 appears 4 Set the pointer input to pointer by selecting it in the popup menu Next Sample C Sampie Delen 5 Use the pointer to identify each electrode When the Aaka Samples pointer is on each electrode click on Sample to record No Samples the location If the sample button is disabled or you hear a beep when sampling either one or both of the pointer and subject trackers are not visible to the Polaris Check that the camera is positioned correctly and try again J 6 When all electrode locations are selected click on the Next Sample MASION Save button At the prompt navigate to the desired ead Sampler directory and enter a file name No Samples 7 Close the window by clicking on the close window but ton USING ELECTRODE RECORDING FOR LOCATOR 1 Locator Electrode Locations 3 When we refer to Talairach space we realy 4 refer to the MNI305 implementati
6. See also tools pointer Pointer lines 38 Manual 51 sphere 38 stick 38 Pointer Mode coil 39 Polaris camera 2 configuration 35 connections 7 Control Window 4 45 location 13 14 maintenance 85 position sensor See position sensor power 7 45 troubleshooting 46 position sensor 13 47 precision test 47 print 43 49 50 project Brainsight icon 26 loading See also open open 35 41 save 41 Q QuickTime movie export 41 50 R Radiology convention setting 11 Rapid Fire annotations 64 coil 41 configuration 83 85 keyboard 40 trajectories 65 using 4042 reference frame 46 reflector spheres 83 85 replacing 83 Registration Task Assistant 35 replacement parts 81 ROM file tracker 3 46 rotate objects 51 Ruler tool 63 control pane 63 S safety xiii sagittal See image view selection save project 29 Segmentation tool 66 79 control pane 67 threshold 67 Index 99 serial number ii 10 software description 43 60 Macintosh application preferences 9 preferences 43 setting preferences 10 12 updates 10 status 46 structures 51 anatomical 66 study preparing and performing 35 targets 33 subject head holder See TMS Frame subject image registration 2 35 See also Assisted Registra tion landmarks 33 v1 0 tool 54 subject tracker 82 fitting 14 fixation equipment 15 surface families 71 setting preferences 72 surface peeler 38 T targeting view See image view selection targets 33 S
7. You will also notice that the orientation as seen in the inline and inline 90 and any tool representation in the 3D view will auto matically orient itself to the normal at that surface Note that in contrast to previous versions of Brainsight objects other than 3D image planes curvilinear surfaces and segmented objects will be invisible to the picking That 1s clicking on a marker on a surface for example will result in the cursor being put on the surface not the surface of the marker itself 3D OBJECT SELECTION There are many 3D objects that can be displayed in the 3D view as shown in Figure 7 11 You can choose what you want displayed any or all of the MPR views oblique views 3D axis indicator trajectory indicator and any annotations In addition you can view any curvilinear or segmented surface created To select an object for display click the box next to the ob ject s name You can select one object more than one object or an entire group To select an entire group the MPR planes for example enable the checkbox next to the group s name You can also hide objects from view by deselecting the object s check box for example if you find that the axis object is in the way you can remove it Coordinate Views coordinates movement and orientation of the view for the panes that have it enabled That is any move ment in one of the 3D views will be applied to any other 3D view where Coordinate Views is active If
8. dust free latex glove to manipulate them Each reflector should be inspected before every use and replaced if any visible dirt or damage is noticed REPLACING TRACKING SPHERES Remove the damaged sphere by pulling it off the post Some force may be required Then using a lint free cloth push a new replacement sphere onto the post until you feel it click into place An improperly placed sphere can have an adverse affect on accuracy or can result in the camera failing to track the tool at all X keys Switch The X keys Switch Interface Figure 9 4 is used in conjunc tion with the coil tool for the Rapid Fire feature of the Marker and Trajectory tools 84 Brainsight 1 7 Figure 9 4 The X keys switch box is programmed to send a specific key stroke such as the key when it receives a TIL trigger pulse The Rapid tire control in Brainsight must be set to trigger on that same key Thus when a TIL trigger is sent to the X keys it sends the keystroke to Brainsight which in turn trig gers the rapid fire tool to record a marker or trajectory X keys Switch Interface Many TMS tools come with a transistor to transistor logic TTL signal feature see Figure 9 5 that allows you to trigger external devices from the coil The X keys Switch device works with this TTL pulse to send a signal to the Brainsight compu ter Brainsight s Rapid Fire keyboard trigger mode receives this signal from the X keys Switch The signal
9. rarerarrrnnrrrarerarennnnnnnre 61 Typical Usage Notes rrarrnnrnarrnnrnannnnrnnrnannnnnnnrnnnn 62 UIE HOOP rer 63 General Description cccecceseeeceeeceeeeeeeeeeeeeeees 63 Control Pane DeSCYription ccscccceceeeeeeeeeeeeees 63 Typical Usage Notes ccceceeeeeeeseeeeeseeeeeeneees 63 Marker Tool ccccccsccscceeeeceeceeseeeeeeecseseeeeeeegeeeeseeaes 63 General Description sssrinin 63 Control Pane Description rrrrrarernrrrnrvrarernnennnre 63 Typical Usage Notes rrrnnrrnrrnnrnnrrnernarnnnrnernarnnnnne 64 TAN Ve 65 General Description eseina i 65 Control Pane Description cccccccceeeeeeeeeeeeeeees 65 Typical Usage Notes ccccccseeceeeeeeseeseeseseneeees 66 Segmentation Tool cccceccseeccceeeceeeeeseeeceeeesseeesaeees 66 General Description rrrrrrarenarernrnvnnnnranenanennnnnnnne 66 Control Pane Description rar rarrrnnrnrarerarennnnnnnre 67 MANUAL SEGMENTATION CONTROLS sunneranevnrnnnrnnnevnnennenn 68 FAST SKIN CONTROLS cccecccseceeteceeeeeeneeeeeseeeneeeeseees 69 Typical Usage Notes ccccceceeeeseeeseeeeeeeeeeeeseees 69 FAST SKIN SEGMENTATION cccceccececeeeeseeseueeeeeeeeeeeass 69 MANUAL SEGMENTATION ccccecceceeceeeeeeceeeseeeeeeeeeeeeeeeees 69 Curvilinear TOOL rerurnnrrnanrnarnnnrnnnennvennnenerenernnnenanenesnn 71 General Description rrrrrarernrernrnnnnnnran
10. 1 7 Els Figure 1 1 E A B A The top image shows proper tracker orienta tion so that it faces the camera The lower illustra tion shows that in the Polaris view all the spheres are clearly visible and do not interfere with each other B Poor tracker orientation results in the camera not having a good view of all the spheres In the lower illustration the camera cannot see all the spheres clearly and thus would not be able to track the subject Figure 1 2 Coil tracker Subject Image Registration Registering the subject means performing a calibration that determines the spatial relationship between the image data and the subject during the experiment Registration is accomplished by selecting a series of common points on both the image data with the computer mouse and the subject with the pointer tool These points are referred to as homologous point pairs These homologous point pairs are used by Brainsight to calcu late the spatial transformation from the subject s head to his or her image data This transformation in turn is used to map the position of tools in three dimensional space to the image space for display Brainsight Terms This guide frequently refers to the items defined hereafter Hardware Terms In addition to the Macintosh computer running the software the following hardware components are integral to the Brainsight product POLARIS OPTICAL POSITION SENSOR The Polari
11. 15 Telephone 1 514 284 3888 Toll Free North America 866 984 38888 Fax 1 514 284 6750 http www roque research com Version 1 7 Brainsight image analysis and Neuronavigation software 2001 2007 Our products are Brainsight Brainsight TMS Brainsight Primate Contents Legal Terms and Conditions xi End User Software License Agreement rrnnnrannnnnn xi LACES RE EE XI Permitted Uses and Restrictions rrarrarrnrvnrvnnvnnrnrr xi CONI A E E xii TN xii SO EEE EN EE xiii Declaration of Conformity rrrarernnrnnerrnnnnranennnennnnrr xiii Manufacturer rrarnarnarnarnarvanvannannannnnnnnnnnnnannennennene xiii Authorized European Representative 00 xiii European Distributor ccccecceeceeceeseeseeseeeeeseees xiii Chapter Overview 1 How This Document is OrganiZed cccseseeseeeeeees 1 Operating System Environment ccceeceeeeeeeeeeees 1 Concepts of Frameless Stereotaxy cccceeeeeeees 1 Subject Image Registration rrrrrrnnreranennrrnnanennre 2 BrainsigNt FORMS eessen ee E E 2 Hardware Terms c cccccceceeceeceeeeeeceeseeeeeeeeeeeeeaes 2 POLARIS OPTICAL POSITION SENSOR scceseeceseeteneeeeneeeens 2 TS 2 TN 3 Software TE 3 TOOL CALIBRATION FILE uuranuernnnvnrnnnvnnnnnennnnnennnnsnrnunennnvee 3 TRACKER CHARACTERIZATION FILE ROM FILE s 000 3 POLARIS CONTROL WINDOW cscccesseeeeeeeeeene
12. 47 Volume View Window rrurnnnenennnnvnnnenenenavnvnnnenenenenener 48 Image Controls rarannnnenranrvnnnevnanennnnennanennnnennnnennnee 49 THRESHOLD CONTROL veces cccnstertinesctecunisensrarseseseseecteaar 49 ZOOM NO 49 LAYOUT SEE WOR kenra rae a tc nenanctautasensoeneqeetacn 49 Image View Pane rrrnnnnnrnnnnnnnnnrnnnnnnrnnnnnnnnernnnnnen 49 EXPORT VIEW TO FILE sverarnrnnnnnansnnnnvnvnnnnnnnsnsnsnnnnnnnnnnenene 49 EXPORT VIEW TO QUICKTIME MOVIE sscceceeceeeeseseeseseeeess 50 PRINT VEN EE EE 50 PIE 50 2D IMAGE VIEW verarnannvnnnanannnnenannnnnnanennnnsnannnnnnenennnnenen 50 VEN SELECTION Lugrmsageameemmdadmmea rden 50 PMOI 51 OW IMAGE VIEW orrn 51 MENN 51 TRANSLATE OBJECTS ananernvnvnrnrnrnrnenennrnvnnnnnensnsnanenennsnrn 51 ROTATE OBJECTS de 51 DU 52 SD OBJECT SELECTION cccececeeeeceteeeteceeeeeeeseaeeeserseanes 52 ORIENTATION SELECTION see 53 Advanced Procedures arrnrnnnnnnnnnnnnnnennernernennernennenner 53 Importing Target Coordinates cccccseeecseeeeeees 53 Using Electrode Recording ccceccseeceeceeeneeees 55 Contents iX Eee USING ELECTRODE RECORDING FOR LOCATOR ccsceceeceeeess 55 Converting To MNI Talairach Coordinate Space 56 Errors and Troubleshooting ccsecceeeseeneeeeeeeeeneeees 58 Chapter 8 Tools and Controls 61 CS TOO ed 61 General Description rrrrrrarernrennrnvnnnnranenanennnnnnnne 61 Control Pane Description
13. Coil on page 38 It might be useful to take a moment and make a small shallow divit on the coils face correspond ing to your preferred hot spot using a small drill bit held between your fingers or using a small knife e g X Acto This will simplify calibration as the coil will clip into place as the pin goes into the divot This will simplify placing the coil over the pin and improve consistency between calibrations Chapter 3 19 3 Figure 3 9 Drep lees Step 4 10 11 Task Assisa Step 4 Perform Calibration Finally Position the calibration block 20 ihat the Positron sensor Gama Gn set Ee Cabbratioan blods spherts Place the coll on the calibration block so that the har spot identifeed in step 1 over tha centre S ke of the Block When ae Call amp in posten the square Below will be green cick on the Lalbrate button belte The solbware will Count down Seconds b tore Ameti Hesp At th poet haka The ood Still until stand beep is produced about 3 seconds W Coil NOT visible E Calibration block visible Calibrate Waiting Go te Previous Step Dane Place the calibration block on a flat surface or attach it to the chin rest assembly on the TMS Frame so that the spheres are visible within the Polaris s field of view and so that the tracker on the coil is in the field of view green square when in the calibration position Examine the calibration block Ensure t
14. Friendlier Preferences and Tool Control Panes The default values given to various preferences are more use ful The control panes for various tools are cleaner more effi cient and in some cases are more powerful allowing you greater options in controlling your data for example for both selecting and removing a subject registration file from a project Chapter l DT Data Groups Window Information Pane This pane indicates the number of markers trajectories surfaces and registrations associated with an image data set as viewed when an image set is selected in the Image Data list This describes a fundamental change in how Brainsight stores its data In previous versions data including markers trajec tories and curvilinear surfaces were kept as part of the View window Closing the window deleted the associated data This is no longer the case and all data is associated with the image data as shown in the Data Groups window Opening a second window for example will inherit any markers trajectories and so on that were created in a different window Closing all Vol ume View windows will not delete associated data To close a project quit Brainsight Command Q or use File gt Reset Project Command N as discussed in the next section File gt New Reset Project menu This menu item clears the current project from Brainsight s memory essentially creating a new project If the current un saved project has any
15. a cortical target will make your procedure more tolerant of small changes in the orientation of the coil For example Fig 8 25 illustrates the coil placed over a trajec tory whose origin is scalp based The trajectory projects into the cortex from the scalp If the position and are perfect then the correct part of the cortex will be stimulated This result is some what indirect like trying to put a key in the lock by tying the key to a long stick A small error in orientation of the coil results in a targeting error in the cortex Figure 8 25 GB Target used for positioning Trajectory used for positioning BG Desired cortex to stimulate Actual trajectory Left image shows a correctly placed coil over a target and trajectory defined at the scalp that projects into the cortex to a desired target Right image shows the same target and trajectory definition but the coil has been placed with an error in orientation Despite being placed on the scalp target a dif ferent part of the cortex will be stimulated Fig 8 26 shows a similar setup where the target was defined in the cortex The left image shows the same target whith a similar orientation error as before Since the user was able to center the coil over the target the only change 1s a slightly different ap proach to target than desire In the end the desired part of cortex will still be stimulated Thus the end result will be more accept able than using a scalp based targe
16. and subject tracker are automatically loaded The Reference Frame as shown in the reference popup menu should be Subject Tracker If not correct your Brainsight Preferences If the Polaris was in use when the project was last saved upon opening your project Brainsight asks you whether to load the Polaris information for the project If you are using the Polaris check yes Note that if you are going to use a newer coil calibration than the one before you must replace the old calibration with the new one To replace the old file with the new 1 Select the old tool Coil in the tools list in the Polaris window Click Remove to remove the old tool 3 Click Add then select the tool calibration file from the file select dialog Chapter 4 Transfer Images to the Brainsight Computer Many MRI scanners can archive images on various media Unfortunately some of these systems use a proprietary format that can only be read by their own equipment Figure 4 1 eoo L Subject Data oo Lb m i y Back Forward View Computer Home 7 itemi 46 64 GE available Name T A Subject Data T L Peter Smith 12345681 b Preop MRI Scan copy ko Preop MRI Scan Y 2 John Doe 12345640 e J MRA Scan 2 gt MBI Scan 1 Example of folder organization for structuring files on the computer hard drive Cc images to the workstation can be done from any of the following sources CD ROM e External dri
17. domain Mac and UNIX based DICOM server applications available that enable you to have image data transferred by DICOM transfer directly to the Macintosh For example you can use OsiriX to act as both a DICOM storage client to transfer images directly from the scanner or to scan a DICOM CD drive to allow you to easiy select the study of inter est from the other files on the CD and transfer them to your hard disk Additional software can be used to automatically convert these images into formats used by other software including MINC and Analyze Contact Rogue Research for more details 22 Brainsight Primate E N You are generally required to have an ac count on the computer system to access information on computers by FIP Ensure that your account has the required privileges to access the images File Transfer Protocol FTP is a nearly universal protocol for transferring files from one computer to another With some organization FTP can be a simple and fast method for transferring MRI images from your scanner or database computer the archive to the Brainsight computer Contact the archive system administrator to find out if they support FTP transfers If the host computer is a UNIX worksta tion it is highly probable that there is a FTP host application running USING FTP TO TRANSFER FILES The steps involved are Il Determine the Internet Protocol IP address of the ar chive server or the computer storing the desired
18. images The IP address can be specified in two forms the IP name based address e g studies edu ca or the actual IP number e g 123 123 123 000 2 Ensure that the archive server has an FTP server applica tion running 3 Obtain a user name and password to allow FTP access to the server 4 Ask for the location of or find the image files on the archive server 5 Create a folder on the Brainsight computer for the image files 6 Run the FTP program on the Brainsight computer to ini tiate an FTP session with the archive 7 Using the FTP software locate the desired images on the archive server 8 Transfer the desired images from the archive to the new folder on the Brainsight computer The first three steps are performed only the first time you transfer images from a particular archive After the FTP applica tion is set up future transfers begin at the fourth or fifth step USING THE FINDER FOR FTP 1 Inthe Go menu select Connect To Server 2 Inthe Address text box type ftp and the name of the server Finder prompts you for a username and password 3 When the server appears on your desktop you can navi gate it as if it were a disk on your computer 4 When you have located the desired file copy it to the prepared folder or another location in your hard disk Copy Files from an External Disk If there is no network connection possible between the Brain sight computer and the archive work
19. marker is selected 64 Brainsight 1 7 E Figure 8 5 Edit Marker Label Colour CA Hilight colour Co er a JD size 200 3D size Cancel Edit Marker dialog Figure 8 6 Preu Tra Inde a Bead time D Lilo 4 Trigger Keyboard Key bd Ker a M Active Ki Raped Fire rato Page i Trea Indera Dead time 01103 Trigger Moute Bink Raced fire mai Prefix Trill ingie Dead ime O LAID a Trigger Labjack f hie ilo hoe te il Arie Rapid Fire Trigger windows Marker tool and Trajectory tool trigger via mouse click key board key typically for use with the X Keys switch interface or using the TTL input via the LabJack interface on certain Brainsight systems This makes it simple to distinguish a particular marker in a crowded screen The Rapid Fire button opens the Rapid Fire window The Rapid Fire option while Active allows you to successively drop several markers with a minimum of interaction with the software interface For more information about the Rapid Fire feature see Rapid Fire Configuration and Operation on page 40 In the Rapid Fire edit box the contents of the Prefix and Index fields determine the names of the markers as they are cre ated For example if the Prefix is Sample and the Index is 1 then the first marker is called Sample 1 For subsequent markers Rapid Fire automatically increments the Index number
20. mount Tighten the set screws to lock the arms on place 13 Add the chin rest horizontal bar by inserting it into the slider mount of the vertical bar Add the vertical bar of the chin rest into the slider receptacle end of the horizontal bar and finally insert the chin rest into the hole at the top of the vertical chin rest bar Figure 10 21 Chin rest assembly 96 Brainsight 1 7 me OPERATING THE CHAIR 1 The chair can reclined by pushing down on the reclining knob on either side of the chair Figure 10 22 Recliner knob Figure 10 23 2 When needed e g when using the chair in the reclined po sition insert the adjustable leg supports by loosening the 2 knobs under the front of the chair and inserting the rail ends of the supports into the receptacles under the chair and tightening the knobs 3 Rotate the chair by pulling the cable under the chair to release the locking pin and while holding the cable rotate the chair The pin will lock at the 0 or 180 positions 4 Move the chair forward backwards by loosening the latch of he sliding block under the chair see Fig 10 17 and moving it forward and backward Figure 10 24 Leg supports Chair in upright configuration Index Symbols 2D view 50 selection 50 tools 50 3D cursor 52 3D objects Selection 52 Window 52 3D reconstruction 30 71 3D view 51 camera orientation 53 tools 51 16 or 32 bit 28 O 1 43 A anatomical str
21. network for either but not both of the following purposes Permanent installation onto a hard disk or other stor age device of up to the Permitted Number of Computers or Use of the Software over such a network provided the number of users does not exceed the number of licenses For example if there are 100 computers connected to the server but the Software will be used on 25 differ ent computers at various times the Permitted Number of Computers for which you need a license is 25 e You may use Brainsight or Brainsight for investigational use You may not use Brainsight for therapeutic applications or surgery guidance Copyright The Software is owned by Rogue Research and its suppliers and its structure organization and code are the valuable trade secrets of Rogue Research and its suppliers The Software is also protected by Canadian Copyright Law and International Treaty provisions You must treat the Software just as you would any other copyrighted material such as a book You may not copy the Software or the Documentation except as set forth in the Permitted Uses and Restrictions section Any copies that you are permitted to make pursuant to this Agreement must contain the same copyright and other proprietary notices that appear on or in the Software You agree not to modify adapt translate reverse engineer decompile disassemble or otherwise attempt to discover the source code of the Software Tra
22. of three error messages appears Figures 7 20 7 21 7 22 Chapter 59 Es Figure 7 20 The serial port is not responding Check that the Polaris is properly connected to the computer and that the correct serial port is selected in the Preferences Then close and reopen the Polaris Control window ox Figure 7 21 No serial ports found The Polaris requires serial port and none can be found on i the computer Please quit Brainsight connect serial adapter connect the Polaris to that serial adapter then retry Figure 7 22 The serial port you have chosen in the Preferences is not currently available Make sure that your USB to serial adapter is connected and that its drivers are installed and up to date or If you receive the dialog in Figure 7 23 you have a version checking error Figure 7 23 There was an error checking for newer releases of Brainsight ie Please make sure your internet connection is working and try again Version checking error 60 Brainsight 1 7 _ SS ees To solve this problem either connect the computer to a net work that connects to the Internet or go to Brainsight gt Prefer ences and turn off version checking in the General preferences Figure 7 24 The data could not be loaded because an error occured The image file may be corrupt or in a format that Brainsight does mot recognise Verify that the image he
23. recom mend v10 5 in order to enjoy all of Brainsight s functionality We assume you are familiar with Mac OS X We no longer support Mac OS 9 If you are new to the Macintosh it would be an excellent investment of your time to take an hour or so right now to go over the Macintosh introduction tutorials A little time now will save you a lot of effort later Remember that the Com mand key has a symbol on it For meanings of terms specific to Macintosh descriptions and usage for example shift click access Mac Help by the Help menu in the Finder Concepts of Frameless Stereotaxy There are many aspects of TMS that are the subject of ongo ing innovation These include the following e Focality of the coil e Power and frequency output of the coil e Techniques to improve accuracy and consistency of coil placement In many neuroscience applications of TMS one stimulates a small set of selected neurons to observe their functional sig nificance Accurate coil placement is necessary however it is difficult to know the exact brain tissue that receives stimulation given the location of the coil on the subject s scalp Brainsight TMS displays the location and orientation of the TMS coil in real time on the magnetic resonance images MRI of the sub ject You can use this display to guide the placement of the coil directly over your desired stimulation site This new way of coil positioning is called Image Guided TMS 2 Brainsight
24. red appears Figure 8 18 enter the information required a surface family name b guide curve plane c quality default is high lower if you have rendering problems d the 2D interpolation to Nearest Neighbour or Linear if you don t know which you prefer use the default value e Optional if using the MinIP or MaxIP renderer set the slice thickness f desired iso distant depths surface offsets Figure 8 21 A B Illustration of the drawing direction for curvi linear surfaces for the two display conventions A Normal B Radiology R indicates the sub ject s right side Figure 8 22 ef Curve drawing grazing the top of the sulci depth generation during reconstruction 0r Chapter 8 13 I Click Add Usually one starts with a 0 mm offset sur face and then enters subsequent offsets for example 2 4 and 6 mm Click Add Series Enter a start depth an end depth and a step size For example enter a start depth of 0 mm and end depth of 20 mm in steps of 2 mm Click OK Draw the guide curves Make sure you draw the curves in the same direction clockwise or counter clockwise as shown by the direction indicator in the top left of the image view The direction of drawing clockwise or counter clock wise 1s dependent on the imaging convention normal or Radiology Figure 8 21 which is set in Brainsight s General Preferences If you are in Radiology mode you need to draw curve
25. the following conditions The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software THE SOFTWARE IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO THE WARRAN TIES OF MERCHANTABILITY FITNESS FOR A PAR TICULAR PURPOSE AND NON INFRINGEMENT IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM DAMAGES OR OTHER LIABILITY WHETHER IN AN ACTION OF CONTRACT TORT OR OTHERWISE ARISING FROM OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFT WARE Chapter I Overview VW come to Brainsight TMS version 1 7 v1 7 This software in addition to being written to support both the PowerPC and Intel based Macintosh computers contains sev eral new features and enhancements over the previous version We hope you find the enhancements useful and we look forward to your feedback as solicited at the end of the manual The Rogue Research development team How This Document is Organized This chapter gives a brief description of terms to prepare the new user for subsequent sections It also describes software en hancements since v1 5 Red text in the content of this manual is text that 1s hyper linked in the PDF version available from the Help gt View User Manual menu Operating System Environment Brainsight requires Mac OS X v10 3 9 or higher we
26. the images along with con 2D View 3D View trols to configure how they are displayed e Controls cms The Tool Bar is where you select a tool 3 Bala eur hE Flelale a e The Tool Controls are specialized controls that change depending on the tool you have selected Image Controls The image controls allow you to manipulate certain image parameters of the data set being displayed THRESHOLD CONTROLS 2D View 3D View This slider allows you to change the Brightness Contrast level of the image data displayed by click dragging on the control 2D and 3D Image View Panes thumbs that is the black triangles If you are overlaying func tional data use the pop up Main Data Set Overlay Data Set showing the name of the data set to select the data set affected by the Brightness Contrast Threshold controls ZOOM CONTROL Zoom control allows you zoom all of the 2D views simultane ously within each layout mode To zoom the views use the slider at the bottom left of the window LAYOUT SELECTOR Brainsight supports three layouts for the image view window The 6 up a 4 up and a l up view You can select the layout by clicking one of the three tabs at the top of the window Image View Pane The image view pane is where the actual image is displayed Controls above the image allow you to configure each view to your needs The image view pane functions in two view modes 2D and 3D The controls for
27. the other software must be in the subject s native MRI space not in a normalized space This procedure is similar to the subject image registration you may be familiar with see Register Subject to Images on page 35 for that procedure Follow these steps Il In your analysis software select at least four landmarks that are easily and accurately identifiable Note their locations and the coordinates shown within the analysis software s coordinate space Also note the coordinates of your target s 2 In Brainsight load the MRI Use the Marker tool to identify the same landmarks as you did in your analysis software except the target 3 Select Windows gt Manual Input A Manual input win dow opens with entry fields for X Y and Z as well as sliders for A P Lat amp twist 4 Inthe Cursor tool control pane select New Manual Reg The Registration Tool window in Figure 7 13 ap pears 54 Brainsight 1 7 773 Figure 7 14 AAC Electrode Recording Pointer Mause ia Electrode Samples No Samples Anatamical Samples No Samples Next Sample LFA Save Electrode Locations Figure 7 13 Manual Registration Pointer Mouse HH Sampled points p D y Registration Tool window 5 Inthe pop up menu in the Registration Tool window select Manual as a Pointer source 6 In the Marker tool double click on the first anatomical landmark to bring the cursor to its locat
28. this box is left unselected the view remains independent of the other 3D views If Automatically Add New Markers or Automatically Add New Trajectories and or Automatically Add New Grids is enabled all markers and or trajectories and or grids that are created will automatically be displayed in the 3D view This eliminates the need to re open the list selector to display newly created markers and trajectories Chapter 93 3 Figure 7 12 ORIENTATION SELECTION ot Camera renmtion This brings up the selection window for the virtual position of the subject The camera view can be moved to a series of pre selected orientations Figure 7 12 Choose from the series of presets by clicking on the desired orientation then click OK Advanced Procedures You may require any of the following advanced procedures in the course of your study M Preview 3 e Importing target coordinates e Electrode Recording a _ Cancel Electrode Recording for Locator 3D camera orientation selection e Converting to MNI Talairach Coordinate Space Importing Target Coordinates You can perform image analysis using other software to find target coordinates for TMS studies For example you can use software capable of displaying functional images over anatomi cal images It is possible to register the coordinate space to the Brainsight TMS coordinate space and translate coordinates from one to the other The images in
29. while the Prefix name remains the same Enabling or disabling the Display in 2D checkbox allows the markers to be shown or hidden The Display labels box displays or disables hides the marker labels on the image If you wish to save the coordinates of the markers to a text file press the Export button Brainsight prompts you for a file name After entering it and pressing Save it creates a file containing the names and 3D locations of all the markers The 3D locations of the markers are stored in Brainsight s internal coordinate space The origin of this space is the anterior infe rior right corner of the image data with the X direction going towards the left the Y direction towards the anterior and the Z direction towards the superior The units are in millimetres To prevent accidental movement of the markers click on the Lock checkbox With the lock on you can select markers by clicking on them without accidentally moving them Typical Usage Notes To drop a marker at the current cursor location click the Mark button in the tool control pane After entering the name and pressing OK Brainsight places a new marker at the cur rent cursor location Alternatively make sure that the Lock checkbox is unchecked and click the mouse in any 2D view A marker 1s dropped at that location Immediately after clicking the mouse you receive a prompt to name the marker Enter a name and press OK Pressing Cancel instead avoids cr
30. ATE OBJECTS This tool allows you to rotate the objects in the view Because rotation is a three dimensional operation and the mouse only allows two dimensions of movement depending on where you click the mouse the movement is different The view is divided into two zones as shown by the yellow circle in Figure 7 10 52 Brainsight 1 7 n Figure 7 11 40 Object Selection Objects to display 7 MFR Tramsverra Tygital Ear n l Hhlique l lene Inline 30 Farpandbcular Harkurs feks d jer 4 4 4 Iraptctories Aleks Prais Ait Lina Pointer iik Pinter Line j Painter vEbhere Figure Coil Coordinate Views iM Automatically Add New Markers W Automatically Add New Trajectories Cancel ok Dialog listing all the 3D objects While the mouse is inside the yellow circle click dragging dragging the mouse while holding down the click button rotates the 3D scene in the direction of the mouse movement If you click drag outside of the circle the object rotates in a twist fash ion as shown by the outer red arrow When you click the mouse look at how the cursor changes If the cursor has a twist arrow it twists the image If it does not have the arrow it performs the grab style rotate 3D CURSOR If you see an object or structure in the 3D view that you wish to examine click on the structure using the 3D Cursor tool The cursor location in both the 3D and 2D views moves to that point
31. Brainsight User Manual version 1 7 9 pa 5 N yo R2 lt TE N PM E B N N V d A d k A ke p 6h OON g 4 as N j d y OG GESEARCH Inc Your Serial Number 1s Ag Er Research Inc Phone 1 514 284 3888 4398 Boul St Laurent 206 Toll Free North America 866 984 3888 Ay Montreal OC H2W 125 Faxe 514 284 6750 GESEARCH Inc E mail info rogue research com Brain TMS User Manual version 1 7 Technical support Rogue Research will provide one year from the date of the invoice unlimited e mail support for Brainsight related problems Rogue Research will provide software upgrades software improve ments and or bug fixes by disk media CD ROM and by Internet and FTP transfer whenever possible Rogue Research will provide one year support parts and labour for manufacturer defects Brainsight is a trademark of Rogue Research Inc Polaris and Vicra are registered trademarks of Northern Digital Inc Macintosh Mac OS and QuickTime are registered trademarks of Apple Computer Inc Intel is a registered trademark of Intel Corporation or its subsidiaries in the United States and other coun tries Velcro is a registered trademark of Velcro Industries B V X keys is a trademark of P I Engineering Inc X Acto is a registered trademark of Elmer s products Inc Roque Research Inc 4398 Boul St Laurent 206 Montreal OC H2W
32. Figure 5 10 Bu Transverse HEGE MG soe alela Threshol To generate a simple skin object l Set the bounds for the skin object by dragging the edges of the green box on the images 2 Sat the threshold controls to select the alr space around the head 4 J Click Segment amp Update aes lf needed move the seed by mrs moving the cursor and click Tweak Seed amp Update THELESS balder F Smooth Image Data Fl Make Smooth Mesh Example of a good result in segmenting the skin The head should be highlighted and the mesh seed should be on the edge of the skin If the mesh seed is off the skin due to noise in the scan move the cursor to the edge of the skin in the transverse view and click on Tweak Seed amp Update Figure 5 12 C Bridge A and tip B of nose and inter tragal notch of ear C on MRI scan Chapter 33 Eee Figure 5 11 Example of a good 3D skin 6 Once the mesh is built the 2D displays should look like Figure 5 10 Set one of the image views to 3D mode then click on the list selector and select the skin The object should appear as in Figure 5 11 7 Ifthe skin object does not appear then verify in the transverse view that the mesh seed an indicator of the edge of the skin is indeed on the edge of the skin If it is not move the cursor to the edge of the skin and click Tweak Seed amp Update This will attempt to build the skin a
33. Figure 5 4 prompts you to select a voxel mapping style Select the appropriate mapping style to load the images If you are unsure which mapping style is best experi ment with the styles until you find the best one 4 For Analyze and NIfTI if the 1mg file associated with the hdr file is not in the same location Brainsight prompts you to find it Locate the file and click Open 5 Ifyou cannot obtain a satisfactory display remove the images from the project by clicking on the data set in the Data Groups window Figure 7 2 and clicking Remove This also closes the Volume View 6 Repeat steps 2 to 5 until you find which style works for your images Take note of this for the future 7 After the images load the Volume View display window opens with the image file name in the title bar Manipu late the image using the Brightness Contrast threshold controls see Figure 5 5 on the lower left of the view window Functional Images After importing anatomical MRI images you can import and then overlay a functional MRI image such as fMRI or PET The functional data must have been preprocessed by your fMRI processing software to register to the anatomical data The func tional data must also have been resampled so that the image file has the same dimensions and orientation as the anatomical data Set When opening fMRI and PET images the Volume View should look like any other anatomical data Volume View win dow There are how
34. Go to Next Step Step I summarizes what we already did in preparing the study It is here to remind you of the steps 36 Brainsight 1 7 773 3 Click Go to Next Step Figure 6 2 appears Figure 6 2 O Task Fissis boil Step 2 Conhgure Polaris Tools This steg tells Bramsight which tools you wil be using to identify the landmarks on the subject and which tracker is on the subject 1 Hike sure that the Pointer and Subject tracer appear in the list below If they are not be sure that you have selected a Tools folder in the Preferences and that the Polaris settings are also correct Consult the User Manual for more info oS Configure Tools 2 Add your coil calibration by Gicking on the Aid Tool button Ska and selecting the calibration file from the dialeg box ible Tale Polet Pointer P 17 bet Add Tool I T Subject Tracker ST568 txt Remove Tool Step Inte Goto Previous Step Go to Next Step Step 2 In this step you configure the Polaris position sensor The list box at the bottom right shows a list of the tools the Polaris will be asked to track The default tools namely the pointer and subject tracker should already be in that list If not this indicates that Brainsight is not configured correctly and you should halt the registration process and verify that the Tools folder in the Default File Paths tab preferences 1s set correctly see Chapter 2 If the pointer an
35. Mount the external disk on the Brainsight computer by inserting it into the appropriate drive or attach it by cable to one of the ports on the back of the Macintosh After a few seconds an icon should appear on the top right area of your screen If after ten seconds or so the icon does not appear or if an error message appears the disk may not be in a format that is supported by the Mac intosh workstation 6 Open the mounted disk in the Macintosh Finder by either double clicking the disk drive icon or clicking on it and selecting the Open item in the File menu 7 Copy the images from the external disk Command click multiple images to select them then drag them to the prepared folder on the Brainsight computer During file transfer a dialog displays the copy progress After it completes the files are ready to be examined using Brainsight 24 Brainsight Primate C a Chapter 5 Preparing a Brainsight Project Because Brainsight saves the entire state of the software within the project file it is inadvisable to work on more than one subject at a time Brainsight does not save files ac cording to subject and cannot differentiate between two separate subjects data or for example between anatomical and functional data If two subject files are open at one time at least one subject project saves with the state of having multiple subject data open he concept of a project in Brainsight is different than in othe
36. NSEQUEN TIAL INCIDENTAL OR SPECIAL DAMAGES INCLUDING ANY LOST PROFITS OR LOST SAVINGS EVEN IF A ROGUE RESEARCH REPRESENTATIVE HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES OR FOR ANY CLAIM BY ANY THIRD PARTY BRAINSIGHT IS A RESEARCH APPLICATION AND HAS NOT BEEN APPROVED FOR ANY APPLICATION BY ANY MEDICAL AUTHORITY IT IS THE RESPONSIBILITY OF THE END USER TO ENSURE THAT BRAINSIGHT IS USED IN ACCORDANCE ANY APPLICABLE LAWS License The Software accompanying this License whether on compact disc or any other media the related documentation and other materials collectively Brainsight Software are licensed not sold to you by Rogue Research Inc The Brainsight Software in this package and any copies which this agreement authorizes you to make are subject to this License The Brainsight Software accompanying this License may include various shareware and other commercial Software whose use is governed exclusively by the terms of their respective End User License agreements Permitted Uses and Restrictions This License allows you to use this version of Brainsight Soft ware in the following manner You may e Install the Software in a single location on a hard disk or other storage device of one 1 computer Permitted Number of Computers xii Brainsight 1 7 Er Provided the Software is configured for network use in stall and use the Software on a single file server for use on a single local area
37. OFF Failure to do so may cause serious damage to the Polaris camera If you use a coil clamp with the TMS Frame be careful not to over tighten it as the coil handle can be damaged due to clamp pressure Declaration of Conformity Manufacturer Rogue Research Inc 206 4398 boul St Laurent Montreal Quebec H2W 1Z5 Canada Product Brainsight TMS We herewith declare that the above mentioned product com plies with the EC Directive No 93 42 EEC concerning Class I Medical Devices in conformance with Annex IV and Annex VII Montreal Canada Roch M Comeau Ph D Authorized European Representative The Magstim Company Spring Gardens Whitland SA34 OHR United Kingdom 44 0 1994 240798 www magstim com European Distributor The Magstim Company Spring Gardens Whitland SA34 OHR United Kingdom 44 0 1994 240798 www magstim com XiV Brainsight 1 7 E The following applies to the software library supplied with the LabJack D A board used for TTL triggering Copyright c 2001 2008 LabJack Corporation Permission is hereby granted free of charge to any person obtaining a copy of this software and associated documen tation files the Software to deal in the Software with out restriction including without limitation the rights to use copy modify merge publish distribute sublicense and or sell copies of the Software and to permit persons to whom the Software is furnished to do so subject to
38. Premio cee arten Add VE k dd teria PL Fr eee ser F J Bere hill Fi berga Fee Sere krf dren UM for bomma Tea Ea 4 Curvilinear Surface Family Preferences The Quality bar is mirrored in the Curvilinear Surface Family Preferences It defaults to high quality It controls the trade off between memory usage and quality for the curvilinear surface Lower the quality if you encounter rendering problems Cornal image with a guide curve drawn along the cortical surface Each control point is shown with an X The Peel slider control allows you to select the depth of the surface you want to view essentially navigating through the lay Figure 8 20 ers EG som alels If Edit Curves is checked the view pane displays the guide T curves Figure 8 19 interpolated curves and guide curve in dicators of the current surface family When you begin to draw any new guide curve a short line appears in the other two per pendicular MRI views see Figure 8 20 These lines are Guide Curve Indicators representing the position of the guide curves within that plane They enable you to find any guide curve for editing The process bar indicates how much of the current surface has been calculated Brainsight calculates only one surface at a time Typical Usage Notes 1 Click New button in the Curvilinear tool control pane 2 In the Curvilinear Surface Family Preferences dialog that Guide curve indicators are in
39. TING A CURVILINEAR RECONSTRUCTION 2sc0sceseeee 30 Add a Skin Segmentation cscccceeeeeeeeeeeeneeees 31 CREATING A SKIN SEGMENTATION 2c0cceceeeesececeeceseeeeees 31 Select Landmarks and Targets ccccsseeseeeeeees 33 EPO 34 Chapter 0 Perform the Study 35 Register Subject to IMAGES ccceccceeeseeceeeeeeeeeeees 35 USING THE REGISTRATION TASK ASSISTANT 000eeceeeeeeeees 35 Posh TAS Olsd 38 Using a Trajectory to place the coll c ccceeeees 39 Record Location of COil arrrrarennnennnnnnnnnranenanennnnnnnne 40 Rapid Fire Configuration and Operation 40 USING RAPID FIRE WITH THE COIL cssceceececeeeeeeeeceeeeees 41 DAVE NE POE 41 Export Images and MOVIES rrarnnnnnnrnnnnnnrnnrnnnnnernnnnnenn 41 Chapter Software Reference 43 MENS je 43 Brainsight rrrernnrnnernnrnnnenernnnnnnrnarnnnnnernnnnnnenennnsene 43 EE EE 43 viii Brainsight 1 7 LCI MMI 44 FAG MD REE EE 44 Data Groups Window rarrnnrnnrrnarenurenernnrrnnvennsernvenesnne 44 Polaris Control WindOW ccscccseeceeeeeeeeseeeeeeeseneeenes 45 WAC Go EEE 46 FICTCLENCE FAME wciwdsnacrntuscsamancatwateasadwidenoautaccmuicdense 46 Tools List and Controls rrrnrerarennrnnnrrarenarnnnrnnnennne 46 ANID FAI o og JE 46 ee gs GE 46 Un 46 Position Camera uuasnegandassaninememadm nvr 47 Precision Test rrrrnrrarnarnarnnrnnnarnnrnannnnannarnennnnnnnr
40. TMS Database od rach arrat E nent FA PEN 13317 4 Documents a ae il EE gi L Boston g Movies Brainsig k Images i Music Lev Tree Brainsight TMS pgi Pictures Development BranchDitf Utilities 2 018 Documents a blirseratrir Filan Hide extension New Folder Cancel i Save Save converted project dialog Creating a New Project Launch Brainsight from the Applications folder or from the Dock if you have a shortcut there When Brainsight launches it implicitly begins a new unsaved project Typically the first step 1s to import images From the File gt Import Images menu select the appropriate file format MINC NEMA DICOM Philips ANT Analyze NIfTI img amp nii A dialog appears showing the image data in the folder you indicated in the default file path preferences Chapter 2 The standard file dialog on the Macintosh has a pop up menu at the top to identify the current folder directory and allow you to navigate to other folders In the appropriate folder if more than one image file is needed shift click the number of files you need it helps to always use a separate folder for each study You can remove any unwanted entries from the selected files list by Command clicking to deselect it Once the files have been selected click Open This initiates the loading sequence For the multi file DICOM format select all the files in the directory by sh
41. The Marker tool constrains the movements of the marker to horizontal or vertical axes while the shift key is held down Trajectory Tool General Description The Trajectory tool stores the position and orientation of the cursor This tool is useful at times when recording the position and orientation of tools are of interest It is similar in functional ity to the Marker tool Control Pane Description For the Trajectory tool control pane refer to Figure 8 7 The Trajectories list box in the tool control pane shows all the trajectories The Mark button creates a new trajectory It brings up the New Trajectory dialog Figure 8 8 where you can change the name size or colour of a trajectory To change an existing trajectory s name size or colour select an entry in the list and click the Edit button or command double click the entry in the list to obtain the Edit Trajectory window Figure 8 8 The Delete button is active when a trajectory in the list is selected Press it to remove the trajectory The Rapid Fire button opens the Rapid Fire window The Rapid Fire option allows you to successively drop several trajec tories with a minimum of interaction with the software interface In the Rapid Fire edit box the contents of the Prefix and Index fields determine the names of the trajectories as they are created For example if the Prefix is Sample and the Index is 1 then the first trajectory is c
42. Window Launch Brainsight Select Window gt Data Groups or open a project file or import some images The Data Groups window Figure 7 2 gives the name of the project file in the title bar in the figure the project has yet to be saved and named lists the images opened in Brainsight as well as information about the Chapter 45 7 markers trajectories registrations and surfaces created and added to each data set Figure 7 2 LAP Data Groups Untitled bproj Image Data List be sure to add anatomical data first roch_mri_corrected mnc Information waterphantom 1 2001 mrimne File aries Trajerraries feylslalbom Surfaces Megigter ta MALS Talairach N Data Groups window The data sets names are the filenames of the images that Brainsight has loaded Double clicking or click once then click View any data set in the Data Groups window opens a new Vol ume View window in the forefront of all other View windows Any other data set in the list that is compatible with this main data set can become an overlay data set This is why it is best to add anatomical data first subsequent data sets are potential overlays and the order matters for the display of data You can minimize the Data Groups window to send it to the Dock and declutter your screen Polaris Control Window Launch Brainsight Select Window gt Polaris Control Two events occur first if the system has been properly connected you will hea
43. additional equipment you can program Rapid Fire to automatically record the coil location each time the coil is fired Once configured the Rapid Fire feature can be triggered in two ways The first method is by clicking on Mark with the mouse The second method is by using the keyboard Select Keyboard from the trigger pop up menu In keyboard mode you can designate any key as the trigger key Enter the character in Figure 6 9 Li aged fire boarder Presi Tra nce Bead time 0 LID 4 Trigger Keyboard Key PE Key a MM Active E ipd fire raean Preta Tru Iran Dead time E J LID Trigger kihte He Biirk Aigai F r iei Prefix index Dead vred 5 1 104 Trigger Labl rk fel frp T ar hoe hi Rapid Fire Trigger windows Marker tool and Trajectory tool trigger via mouse click key board key typically for use with the X Keys switch interface or using the TTL input via the LabJack interface on certain Brainsight systems Chapter 6 4 I the key value field then click the Active checkbox to enable it The third method uses a LabJack interface box included in certain Brainsight systems You can connect the TTL trigger to the stimulator device if it has a TTL trigger out or by using a foot pedal or hand held switch USING RAPID FIRE WITH THE COIL l After launching Brainsight and performing the subject image registration select either the Marker or Trajectory tool whichever you wish to re
44. ader data is correct or contact Rogue Research for assistance Ca Analyze file mismatch error This dialog usually occurs when the header of the Analyze image file is incorrect If you selected a header file hdr make sure it is the correct one for the data images it imports or you choose to import The following Figures 7 25 and 7 26 are self explanatory and will receive more attention in future documentation Figure 7 25 Too few files were selected To import DICOM images you must select every file you are interested in not just one file even if the others are in the same folder Figure 7 26 The project cannot be opened This may be because the images used by the project were moved and cannot be found or it may be because the project is corrupt Chapter 8 Tools and Controls Figure 8 1 he Brainsight Tool bar see Figure 8 1 provides the main Tool bar the control pane below the six icons changes according to the selected icon Figure 8 2 Tools Input Mode Mouse HH v Live Distance To Marker Selected none Distance nia Closest none Distance mia Current Registration Brainsight to Cursor tool control pane interface between you and the software The Tool Bar con tains the six following tools Cursor e Ruler e Marker Trajectory Segmentation Curvilinear Cursor Tool General Description This tool contro
45. age data for the head The goal is to colour fill all the air and none 32 Brainsight 1 7 CLI of the scalp Note that there will be structures within the head that have similar intensity values and will highlight as well Figure 5 9 Enable the Smooth Image Data and Make Smooth Mesh available for isotropic data only 4 Itis often desirable to segment a subset of the entire head For example we are usually only interested in the Figure 5 9 WO oses alala BG sona 4 Tea Tso Gey Teneo Reign Ta generate a simple skin object 1 Set the bounds for the skin object by dragging the edges of the green box on the images 2 Set the threshold controls to select the air space around the head 4 if needed move the seed by moving the cursor and click Tweak Seed Lind are MI Srooth Image Data fl Make Smooth Mesh Example of a good threshold selection purple of the area surrounding the head and the bounding box limiting the reconstruc tion to the relevant part of the head area of the head that encompases the face nose eyes and the ears Set the limits of the reconstruction by dragging the upper and lower horizontal lines of the bounding box in either the sagittal or cornal views so that only the face is inside the bounding box Figure 5 9 Click on the Segment amp Update button to initiate the automatic segmentation and mesh building function The process may take a minute
46. alled Sample 1 For subse quent trajectories Rapid Fire automatically increments the Index number while the Prefix name remains the same For more information about the Rapid Fire feature see Rapid Fire Configuration and Operation on page 40 Enabling or disabling the Display in 2D checkbox allows the trajectories to be shown or hidden The Display labels box dis plays or disables hides the trajectory labels on the image The Convert to marker button enables you to create markers based on trajectories with a user defined offset along the trajec tory Use a unique Prefix for markers created by this tool so you do not confuse them with other markers 66 Brainsight 1 7 Typical Usage Notes Use the Trajectory tool whenever you wish to store a trajec tory position and orientation in the volume You typically use this tool to record the location and orientation of the TMS coil during a stimulation experiment To record a trajectory click the Mark button in the tool s control pane The box in Figure 8 8 appears To select a trajectory click on its name in the list double click on it to orient the views of the Brainsight window to that orientation To delete the trajectory select it in the list box and press the Delete button in the Control pane To change the colour of a trajectory Command double click on the entry in the list and change the colour in the corresponding window When you cl
47. amily and the concentric sur faces seem to expand in size rather than contract or vice versa you drew the curves in the wrong direction Delete the surface and start again paying attention to the red curve drawing indicator in the top left of the view e If you want to remove a surface family select the Sur face in the Surface Offsets panel and click the Remove button Grid Targeting Tool General Description In many TMS applications it is necessary to perform a map ping operation where one or more stimuli are delivered sequen tially to a grid of points covering an area of cortex For example you may want to stimulate a series of points over a motor area while measuring the MEP response The grid tool allows you to place a grid of any dimensions over an area of the brain and use it as a template to create a series of markers or trajectories on the scalp as defined by the skin segmentation or the cortex as defined by a curvillinear reconstruction It is important to keep in mind that when creating and manip ulating a grid you are essentially preparing a template You are not manupulating Markers or Trajectories directly but rather you are manipulating a template that you will use to create a series of Markers or Trajectories in the last step Figure 8 24 Grids New Delete Edit M Display in 2D Display labels vi Persistent Display Control pane for the grid control Chapter 8 1 7 Contr
48. and marks 34 Brainsight 1 7 LCI Figure 5 13 Registration landmarks and simple motor cortex target shown in 3D view with skin and brain As with the registration landmarks use the 2D views and the 3D brain reconstruction to identify your target s and using the Marker tool record the target s While this was not covered in this short tutorial targets can also be selected by superimposing functional image data as well as by using MNI305 Tailarach coordinates See Chpater 7 for more details on registering your images the MNI305 space Quit the Project When quitting the project File gt New Reset Project File gt Open Project or quit the application Command Q Brain sight asks you if you want to save the project This eliminates the possibility of accidentally quitting the application without saving your work At this point you are ready to perform your study You can quit Brainsight if you are not immediately continuing to the next section proceeding with subject image registration Chapter b Perform the Study hen it s time to perform the study open the project see Reload a Project on page 25 Notice that the windows return to the state they were when the project was saved at clos ing If you are planning to perform several TMS sessions with the same subject and want to keep the session data separate after loading the project treat it as if it were a template and select Save as
49. at the selected tool is visible or not start tracking by clicking the ON button in the Polaris Control window 5 Click on the Position Camera button A new window opens with a representation of the camera s calibrated volume pyramid silo or Vicra depending on which cali bration is in use 6 Place the pointer in the area where you intend to use it during the subject image registration and notice the dot representing the pointer in the two views on the screen See Figure 7 4 Use this display to position the camera so that the tool is well within the volume CHOOSING THE SUBJECT TRACKER The subject tracker should be fixed onto the subject s head so it cannot move during the study nor interfere with the TMS coil or any other objects on the subject s head for example EEG electrodes Brainsight comes with two methods of fixing a tracker onto the subject a head strap or modified glasses Fig ure 3 2 In either case the tracker is attached to the head strap or glasses by a small hex rod which fits into a collar on the tracker and another collar on the head strap or glasses To insert the hex rod into a collar follow these steps 1 Use the small hex key included in your tool box as list ed on page 81 to loosen the small set screw in the collar see Figure 3 3 enough to fully insert the hex rod into the collar Be careful not to loosen it to the point where it might come out 2 Insert the hex rod fully in
50. ays necessary to do this procedure for an experiment but most users find it helpful Use the Curvilinear Tool to draw guide curves on MRI slices which the tool uses to construct a 3D model of the brain based on the image data that intersects with the guide curves The Peel depth function displays image data at various depths from the surface generated by the guide curves These depths are called offset surfaces CREATING A CURVILINEAR RECONSTRUCTION Refer to Curvilinear Tool on page 71 for the dialogs and descriptions 1 Click the Curvilinear tool button 2 Inthe tool control pane click the New button A dialog appears Figure 8 18 3 Enter a name for the surface family 4 Select the plane in which you want to draw the guide curves It is the coronal plane by default 5 For more settings see Curvilinear Tool on page 71 Enter the desired surface offsets series of curves in one of the two following ways a Click the Add button Enter the desired depth offset then click OK Usually one starts with a 0 mm offset surface and then enters subsequent offsets for exam ple 2 4 and 6 mm OY b Click Add Series Enter a start depth an end depth and a step size For example enter a start depth of 0 mm and end depth of 20 mm in steps of 2 mm Click OK Find a view showing the orientation you selected as your reconstruction plane it contains a curved arrow Create a guide curve Do not place contr
51. between the ends of the ruler and the length in millimetres is displayed between the two ends The Ruler tool constrains movements to the horizontal or ver tical axis while the shift key is held down Marker Tool General Description Use the Marker tool whenever you wish to place or drop a marker in the volume In this way you can recall recorded locations for later review such as landmarks for subject image registration or targets When the tool 1s active you have three ways to drop a marker e Clicking the Mark button when the cursor is over the desired spot e Clicking the mouse within a 2D view over the desired spot only if Lock checkbox is disabled e Using the Rapid Fire feature when tracking a tool Control Pane Description For the Marker tool control pane refer to Figure 8 4 The Markers list box in the Tool control pane shows all the markers Clicking on a marker in the list will highlight it in the list and in the 2D and 3D views by changing its colour to the highlight colour Double clicking on a marker snaps the cursor to the marker s location The Mark button drops a marker at the cursor location Both the Mark and the Edit buttons bring up the Edit Marker dia log as seen in Figure 8 5 This allows you to change the name 2D and 3D sizes and colour of the marker The normal colour is displayed when the marker is not the selected marker in the list while the highlight colour is used when the
52. colour MN Dale 300 Due 200 Currabure ja Trajectory Twist a Update Trajectory Copy To Trajectories Copy To Markers Grid configuration screen You can edit all the relevant parameters for the grid Figure 8 29 Moving the A P Lat and Twist sliders can be used to tweak the orientation of the grid Step 4 Select the grid tool and create a grid by clicking New in the tools control pane As soon as you click on the new button a few things will happen First a window will open allowing you to view and edit key parameters of the grid Figure 8 28 Next you should see the grid in its default format appear in the 3D view and in the oblique 2D views Step 5 Set name the number of rows and columns as well as the spacing between the rows and columns You can enter a different number of rows and columns as well as different spacing for the rows and columns The colours and sizes will be applied to all the nodes in the grid Step 6 Use the AP and Lat angle sliders to tweak the overall angles of the grid to ensure that it is normal to the surface Normally the angle should have automatically be set to the normal This is an approximate value and can be adjusted to accommodate for the overall curvature of the surface under the entire grid Fig 8 29 illustrates the concept Step 7 Use the twist angle slider to rotate the grid until you have the desired orientation Once the orie
53. cord 2 Click on the Rapid Fire button in the tool control pane A Rapid Fire Trigger window as shown in Figure 8 6 ap pears 3 Enter the name and index number you wish to use as a template name for the markers 4 Select Mouse in the trigger mode pop up menu in the Rapid Fire window 5 If you are using r MS and the X Keys or LabJack trig ger mode see below then enter a dead time value that is slightly longer than the pulse train duration e g I second or 10 1 10ths of a second since the field is in 0 1 sec increments This will allow the rapid fire to trigger on the first pulse and ignore the other pulses in a train to minimize the number of recordings to a number that is relevant you only need to store the first pulse 6 When you are ready to record a location click on the Mark button This creates a new marker and the index value in the window increments for the next marker 7 Save the project for later review To take advantage of the X keys Switch to drop Rapid Fire keyboard annotations see Connecting the X keys Switch on page 84 To use the LabJack interface see Connecting and con figuring the LabJack interface on page 84 If you have recorded the coil position during the study save the project file before you quit Brainsight Also if you are planning to review the data off line close the Polaris Control window before the last save so that it cannot automatically open and configure t
54. count There are no user specific preferences Figure 2 5 Brainsight m dr a A Brainsight TMS app 7 L Talairach Template Fi 2 average305 tl D average305 tl ey brodmann mnd T T Tools j 8564 rom CES64 rxt coil2 Coilalibration fl CT266 rom Lik LOTOOS rom an NIRS optode Arras ul P670 rom PETO txt Fn T402 ram i ST402 tat en lf items 04 47 GB available Typical Braisight folder structure Chapter 2 9 Er Figure 2 4 Ener 6 MAD meals ME r E JA inarang hrs neu ons rf Brainabghe TRIS Rear Moter Talairach Templuse Fey A wy e Polar Firmw r Updater heat Crash Rinit 17 1 Reeds UGS Seria sidigi Palais viera FTE USE Inter loii 2 0 pkg eral Driver 22 0 p g Far installation rsinclions please see the Trstalason retncbons dr file Mounted disk image 3 In the Applications folder of your hard disk navigate to or create a folder called Brainsight Open the CD or disk image and read the installation instructions Optional Install the Smart Crash Reports application This will enable you to send a crash report directly to Rogue Research if for any reason Brainsight crashes This may allow us to reproduce the problem and provide faster updates Open the Brainsight folder if there 1s one Drag the Brainsight TMS application file and the Ta lairach template folder into the Brainsight folder you created or opened in step 3 Th
55. cut in the region to fill the region e Cut Line and Clear Region work together to clear a re gion incorrectly filled by a seed fill It functions in the same way as the Add Line Fill Region tools except that they clear selected pixels rather than select them e Clear Slice will remove all seeds and selected regions from the slice Use this tool if some seeds have migrated as you move from slice to slice outside the region of interest and you want to clear the slice and drop new better located seeds and move on Invert allows you to invert the segmentation selection of the volume For example you may set a low threshold and drop seeds in the surrounding area outside the head the air and them Figure 8 13 Q Original Image Threshold Displayed Seed Applied Illustration of the threshold seed process Chapter 8 69 I propagate that throughout the volume Clicking invert will invert the selection selecting the head and clearing the air This func tion 1s most useful in segmenting the skin manually in instances where the automatic fast skin function fails due to image vol umes that are inhomogeneous Mesh Seed places a mesh seed where the cursor is located For best results position the cursor by command clicking as close to the edge of the segmented area as possible use the Zoom to help you with this and then click Mesh Seed If you drop the mesh seed in a bad location you can simply move the cursor an
56. d click Mesh Seed again to move it to the new loca tion Update mesh allows you to create a 3D surface based on the segmented voxels using the mesh seed as the starting position Fast SKIN CONTROLS The Fast skin controls are much simpler than the manual con trols The Segment amp Update buttons initiates the automatic process of segmenting the volume within the box delineated on the 2D views using the threshold range set by the threshold controls Once segmented a mesh seed is dropped at the lower edge of the segmented voxels and the marching cubes function 1s initiated If the initial attempt to Segment amp Update yielded an ac ceptable segmentation but the seed was improperly placed the Tweak Seed amp Update button allows you to tweak the seed loca tion and restart the marching cubes step Typical Usage Notes Fast SKIN SEGMENTATION The Fast Skin segmentation is described in the tutorial Chapter 5 MANUAL SEGMENTATION Some steps in this procedure depend on what you are at tempting to segment If the structure has a clear range of in tensities that differentiate it from surrounding structures then the segmentation process will mostly involve setting the upper and lower thresholds to select the intensity range correspond ing to the structure of interest and dropping seeds in the area If the structure has similar intensity values as the surrounding structure then you will have to depend more o
57. d subject tracker are present and you intend to use a tracked coil click on the Add Tool button and select a coil calibration assuming you have calibrat ed a coil as described in Chapter 3 The coil should now appear in the list You can remove a tool other than the pointer and subject tracker by selecting it in the list and clicking the Remove Tool button 4 Click Go to Next Step Figure 6 3 appears Always try to hold the pointer in such a way as to show the top of the spheres to the position sensor camera Never look away from the subject while you are using the pointer tool This is to prevent the pointer drifting off target or pushing into the skin while registering the subject which can yield a poor registration and an uncomfortable subject Chapter 6 3 I igure 6 3 Task Assistant reps Step 3 Identify Registration Landmarks This is the step when the actual negistration i performed Kine an sstart help you The software will bring the curser to Kaneimarts you identified previously Do one of the following 1 OF it is registration landmark observe the location on the Le images and bring the pantar to the kocation on the subject When Fr you have the pointer exactly on the spot hiver the assistant press the Sample Point butten SSS SE i a ii sample Point 2 Fit is not registration landmark press Sop Point to proceed to the neat point ar press Go To Newt Step if a
58. data in it this command also prompts you to save it before it is cleared Segmentation Tool This is not a new tool It has been a work in progress since v1 0 It can be used to segment structures of interest and create a 3D mesh for viewing in a 3D image view pane in order to sim plify their identification Skin can be segmented to ease subject image registration See Chapter 5 Add a Skin Segmentation on page 31 for more information Task Assistant for Talairach registration This assistant is available through the Data Groups window It allows you to co register the subject s MRI to MNI Talairach coordinate space This allows you to easily use Talairach coordi nate targets for stimulation or determine Talairach coordinates on any marker recorded during a study session Brainsight requires you to first set the default Talairach template file in the preferences This file is provided with the software Annotations Annotations from v1 5 of Brainsight are now specifically called markers in v1 7 and the Annotation tool is now called the Marker tool Annotation is now a general term for both markers and trajectories Convert to Markers This new function of the Trajectory tool takes the trajectories and projects them a user defined distance into the brain You can access this tool from the Trajectories tool control panel 6 Brainsight 1 7 New LabJack DAQ Trigger Input Support As of v1 7 7 Brainsight now
59. date to see which one is most compatible with your EEG analysis software Using the wrong format can lead to 2 mm of error in electrode locations 9 Close the window when you are finished Converting To MNI Talairach Coordinate Space Brainsight provides a simple conversion procedure that results in a conversion from MNI Talairach co ordinates to Brainsight coordinate space and displays co ordinates using both systems in the Volume View window The transformation used is a sim ple affine transform and may not be suitable for all applications If you require accurate Talairach co ordinates you must reverify your data using your preferred Talairach software First in order to use Talairach co ordinates on your data in Brainsight set the default Talairach template file in Brainsight s preferences We provide a verified file average 305 tal lin mask mnc for this purpose l After setting the preferences import your subject data into Brainsight 2 Goto the Data Groups window and select the data in the Image Data list 3 Click the MNI Talairach button The Talairach Task Assistant appears 4 As the task assistant describes use the cursor to locate the anterior commissure and use the Set AC button to set it See Figure 7 16 Figure 7 16 E Tiik Adittant Wie the Gurker f a idomi the anterior and posterior comenissures and ee use the respective See eel Det butoni 15 record them Set AC
60. demarks shall be used in accordance with accepted trademark practice includ ing identification of trademark owner s name Trademarks can only be used to identify printed output produced by the Soft ware Such use of any trademark does not give you any rights of ownership in that trademark Except as stated above this Agree ment does not grant you any intellectual property rights in the Software Transfer You may not rent lease sublicense or lend the Software or Documentation You may however transfer all your rights to use the Software to another person or legal entity provided that you transfer this Agreement the Software including all copies up dates and prior versions and all Documentation to such person or entity and that you retain no copies including copies stored on a computer Brainsight is a trademark of Rogue Research which may be registered in certain jurisdictions All other trademarks are property of their owners Legal xiii Safety Never look away from the subject while you are using the pointer tool Use both hands to steady the pointer as you regis ter the landmarks For this reason you should have an assistant interact with Brainsight while you register the subject Do not reposition major components of the TMS Frame while the subject is in place Components can slip and personal injury can occur Always connect the power cable to the Polaris optical position sensor while its power switch is
61. e coil for coil calibration Two pins are to help you line up the axis of the coil and keep it stabi lized over the plate during the calibration process Their height can be adjusted up or down to accommodate different coils See Figure 9 1 Included with the calibration block is a lug bolt for installation on the underside of the block so that the calibration block can be installed into the TMS Frame receptacle normally used for the chin rest This is practical as the TMS Frame is often already placed in the field of view of the Polaris and it holds the cali bration block stable while you use both hands to steady the coil during calibration Pointer The pointer tool is used to identify anatomical landmarks on the subject and to verify the subject image registration It con sists of a narrow metal shaft connected to a handle which also holds three reflective spheres See Figure 9 2 Handle the pointer with care as the accuracy of the system depends on the pointer shaft being straight If it gets bent con tact Rogue Research 82 Brainsight 1 7 N Figure 9 3 Coil Handle Ring Coil tracker Coll Tracker Figure 9 2 Pointer tool and various trackers Coil Tracker The hardware to track a coil consists of three parts e coil tracker which is a triangular array of three spheres e coil specific coil handle ring sometimes referred to as a coil handle collar hex rod Refer to Figure 9 3 The coil ha
62. e coil holder arm is articulated and can be locked in place by tightening a single knob in the middle of the arm Figure 10 11 The forehead rest can be positioned to accommodate varying head sizes and experimental setups The coil arm is de signed to maintain a constant position of the coil over the target without you having to hold it ideal for long experiments where you would have difficulty holding the arm for the duration Clutch Engage Release Tighten The lever handles have a clutch mechanism Figure 10 12 so Loosen that when you turn the crank into obstruction with the frame you can pull out the sleeve of the clutch and turn the lever han Clutch mechanism dle back to the starting position without turning the bolt This is like a ratcheting action 92 Brainsight 1 7 3 Setting Up the TMS Chair Coil Holder Third Generation System Figure 10 13 New TMS Chair with TMS coil holder arms Figure 10 14 Open Butt joint ASSEMBLY 1 2 Carefully unwrap all items and lay them out on the floor Note that parts are joined using one of two methods The first is by using a double butt joint while the other uses standard bolts and T nuts In both cases T bolts are slid into the slots of the extruded aluminium In the case of the butt joint the joint is secured by tightening the bolts embedded in the slot see figure 10 14 using a 1 4 allen tool while the standard bolts are tightened using the 3 16
63. e folder file structure of your Brainsight installation should resemble that of Fig ure 2 5 If this is a new installation drag the Tools folder into the Brainsight folder as well Do not do this for an upgrade You will delete any pre existing coil calibrations if you do If this is an upgrade from an older version of Brainsight delete the Brainsight Frameless application as we have changed the name of the application to Brainsight TMS 10 If this is an upgrade from an earlier version of Brain 11 sight Frameless please note that you no longer need the files Figure8Box 3dmf Sphere 3dmf or TrajectoryStick 3dmf Feel free to delete them from the Tools folder To create a shortcut to the application on the Dock drag the Brainsight TMS application from inside the Brain sight folder onto your dock This will not move the appli cation but add an icon to the dock for Brainsight TMS If you have a shortcut on the dock for an older version of 10 Brainsight 1 7 mr Brainsight remove it from the dock by dragging the icon off the dock onto the desktop Obtain Software Updates Periodically Rogue Research releases updates to Brainsight either to enhance functionality or address customer feedback The Check for new Brainsight release in the General prefer ences checks for you on schedule or you can click Check Now You can also check for and download updates from the Rogue Research web si
64. eating the marker To select a marker click on its name in the Markers list To delete a marker select it in the list box and click the Delete but ton or press the Delete key To change the colour of a marker Command double click on the entry in the list and change the colour in the corresponding window With Rapid Fire mode you can use a keyboard trigger in conjunction with an external USB device such as the X keys Switch to trigger recording of markers from the coil signal In rTMS applications it may be desirable to record the first pulse of a pulse train and ignore the rest of them Set the Dead Time to a value just higher than the pulse train duration to ignore the remainder of the pulse train 9 Figure 8 7 Trajectories T Mark Delete Ea Edit Rapid Display in 2D N Display labels a Export Convert to marker Trajectory tool control pane Figure 8 8 New Trajectory Label Trajectory l Colour Hilight colour eri 2D size Li no ID size 1 00 Cancel 4 oc 4 Trajectory edit window Chapter 8 65 I If you are not happy with the location of a marker you can move it without having to delete it Disable the Lock checkbox then double click on the marker entry in the list which snaps the cursor location to that of the marker Then in any 2D view click and drag keep the mouse button down the marker to the desired location
65. ed as described in chapter 3 Remove a tool by selecting the tool in the list and pressing the Remove button Calibration File This displays the current tool calibration file for the selected tool Each tool has a characterization file as described in Chap ter 1 This file contains the offset information and the name of the appropriate passive tracker characterization file rom file When you select a tool calibration file it loads along with the rom file Tracker ROM File This field displays the name of the rom file associated with the currently selected tool Status While tracking status information is returned with each position sample The key information here 1s whether the tool 1s visible or missing or if the reference tool is visible or missing These are dislayed using green red indicators green represent ing visible and red representing missing Chapter 4 7 Position Camera This button opens a new window figure 7 4 with a represen tation of the camera s calibrated volume pyramid silo or Vicra depending on which calibration is in use as well as the location of the currently selected tool within that volume See Determin ing the Camera Location on page 13 for an example of its use Figure 7 4 Polaris Positioning Aid Top view Side view Dan Position representation of a tool that is in the calibrated volume Vicra volume in this example Use this display
66. ee also markers study 33 Task Assistant 5 Coil Calibration 16 20 Registration 35 40 threshold Brightness Contrast 49 Segmentation 67 Window 67 TMS accessory mounting frame 87 coil 7 15 See also coil experiment 13 Frame 7 Frame assembly 87 96 TMS Frame TMS 87 96 tool Annotation 63 calibration file 3 46 Ruler 61 63 Segmentation 66 Trajectory 65 Tool Bar 61 tool box 81 tool calibration file 3 tools 3 85 100 Index Er 2D view 50 3D view 51 coil 3 46 83 pointer 3 tracker 2 85 coil 2 15 82 ROM file 3 46 subject 2 14 15 82 83 tracker glasses 85 See also subject tracker tracker spheres See reflector spheres tracking on and off 46 status 46 trajectories Rapid Fire 65 recording 40 Trajectory tool 65 control pane 65 Transcranial Magnetic Stimulation See TMS translate objects 51 transverse See image view selection troubleshooting Polaris 46 U UNIX FTP 22 operating system 22 V v1 0 calibration 44 Registration Tool 54 viewer orientation selection 53 view mode See layout selector Volume View 48 voxel 28 W window 3D Objects 52 Brainsight Preferences 11 Curvilinear Surface Family Prefs 30 72 Data Groups 44 45 Electrode Locations 54 Electrode Locations for Locator 55 file transfer progress 23 Open Project 26 Polaris Control 4 Polaris Positioning Aid 47 Registration Tool 54 Threshold 67 Volume View 48 X X keys Switch 83 85 connecting 84 X Y andZ 44 53 58 64 Z
67. eeeeeeeeenseeees 4 What s New List of Upgrades cccceeeeneeeeeeeeeees 4 Automatic Update Notification rrarrrarrarrnnrnannnnrr 4 Friendlier Preferences and Tool Control Panes 4 Data Groups Window Information Pane 5 File gt New Reset Project menu csecceeeeeeneeees 5 vi Brainsight 1 7 Segmentation TOO ccccccccsececeeesseeceeeeeeeeseeeeees Task Assistant for Talairach registration PAI 9012 1 6 g EEE Convert to Markers cccccceecceeeeseeeceeeeeeeseeeeaees New LabJack DAQ Trigger Input Support Chapter 2 Installing Brainsight Install and Connect the Hardware cccececeeeeeeees POLARIS cccccccccccccccaccucccuccecacuuanuucuuecueuuuevaeueeeuuuacnenas POALRIS VICRA ccccecccccccccccucccuaueccuauuaueuauenuuecueauesuueans Mistal ES Ea 0 seuss neccsresioonccectataae ccsennaancancetianseutenacdmennenat INSTALLING BRAINSIGHT SOFTWARE ccseccceseeeeeeeeeeneeeneees Brainsight First RUN rarvnrenernnrnnrenernnrvnrrnnrnnrnnernnrnneene SETTING PREFERENCES gaa Chapter 3 Planning a new TMS study EET AN DETERMINING THE CAMERA LOCATION eseeeeeeeeeeeneeees CHOOSING THE SUBJECT TRACKER cceeeeeeeeee seen eeeneeeees Configure the Coil for USe rrrrrrrararnnrenrarernnrennanennnrr Attach the Coil Tracker rrrnnnnnnnnnnrnnnnnnnnnnrnennnnnvnenn ATTACHING THE COIL TRACKER cceccs
68. eld an unreliable connection Connect the power supply to a power outlet and the other end to the dongle Note that the power supply does not have a switch so the Vicra should power up at this point After a few seconds you should hear the Polaris characteris tic beep sequence This indicates that the Polaris has successful ly reset itself and is ready for use warm up time notwithstand ing If you do not hear that sound refer to the Polaris System Guide for more information Turn on the Mac by pressing the power button on the Mac intosh computer In the case of the cart based system you will have to open the rear door to access the power button Turn the two thumb screws at the top of the door one quarter turn coun ter clockwise then tip the door towards you and lift it off the guides Install Brainsight You must have Administrator privileges to install software on your Macintosh INSTALLING BRAINSIGHT SOFTWARE Il Log into your Macintosh user account 2 Do either of a Insert the CD into the optical drive If you are using a tray loading not slot loading CD drive and it does not have an open button use the eject key on the key board number pad Or b Double click the downloaded dmg file to mount the disk image See Figure 2 4 If you have multiple Brainsight users on this Macintosh keep in mind that the application preferences can be changed by each user and the changes affect every user ac
69. enanennnnnnnne 71 Control Pane Description rarrrarrrnnrrrarerarennnnnnnre 71 Typical Usage Notes ccccccceeeseeceeseeseeeeeeeeees 72 Grid Targeting TOOI cccccccsececceeeceeeeeseeeseeeesaeeesaeess 74 General Description ccccccceeeeeeeeceeeeeeeeeeeeeeees 74 Brainsight 1 7 Control Pane Description rarrrarrrnnrrrarernrrnnnnnnnre 75 TYPICAL USAGE NOTES 1 cceccecceccaceccceccccccccaccaceaceaees 75 DETAILED STEPS ccccececcececcececcacececcacececcsteceauseacsueas 75 Chapter 9 Hardware Reference 81 Hardware Components ccceccseeceeeeeeeeeeeeseeeneeeeenes 81 VIP 81 Calibration Block rearnnnnnannnnnnnnnnnnennnnnnnnnnnernennenee 81 FONT 81 CI 2 eeror ea NOE E ES 82 METTE 82 Relectior SPNGCI CS secs ccesccdecedcctscseedevaduesdusesdaced etensevees 83 REPLACING TRACKING SPHERES esececeeeecececevevaveveueesenes 83 TREY SO WG EE EEE 83 CONNECTING THE X KEYS SWITCH ccecececeeeeeeeeeeeeeeeevans 84 LabJack Interface ararnnnrnnnrnrvnernvnnnnnnernennnnenevnenene 85 Maintenance igiwseassevstscamsantrneseniasevainavesarsadvensewaresesnencaes 85 Polaris Optical Position Sensor rrrrrrvrnrvvvrvrrnrnn 85 Tracker Spheres rarnnnrnnrrnnnnnannnnnnnnrnannnannnnennnennne 85 Trackers and TOOIlS rarranannrnavnnnnnnnnnnannnnenavennenennene 85 FICE OU A 0 etesnsdennnanaanedenrne 85 Tracker GASSES wiviscstersectcnstnescgntuopiseeaedeinsanr
70. ends of the bars to protect the user from scrapes and provide an aesthetic finish to the frame See Figure 10 7 Figure 10 7 End caps 90 Brainsight 1 7 E Some sticking is normal as there is a bit of Using The Frame For Subjects Sitting Up lay that can cause the accessory bar to l Assemble the horizontal head holder bar by placing the ia ana chin rest bar on the end and sliding the bar into the become 5 lightly tilted while dane which holder on the horizontal accessory bar on the frame causes it to stick When raising the bar tr t i b T id i J ibl 7 2 Place the forehead rest articulated arm into the accessory O False DOU sides s eventy s possibie mounting block and position the forehead rest as desired It should resemble Figure 10 8 Figure 10 8 Figure 10 9 Assembled TMS head frame Alternatively for subjects lying down a head rest can be Head rest which mounts on the accessory mount used See Figure 10 9 for the head cradle for supine position ing bar and Figure 10 10 for the head holder with a facial cradle for the prone position Chapter 10 9 A Figure 10 11 Figure 10 10 Coil Clamp entre Knob Secures These Joints Coil arm articulation Prone head rest on accessory mounting block Figure 10 12 REPOSITIONING THE TMS FRAME Do not reposition major components of the TMS Frame while the subject is in place Components can slip and personal injury can occur Th
71. entered the required information the Threshold window appears as shown in Figure 8 13 Figure 8 13 Thrrsdid J EE Fant Sari Seed Area a Acid Line Prev Slice C AII Regi ee Mest Shite LU HER Line CV Chear Regeon j imn a Thensiaidl Clear Slice eon Teppe er Ty Bre iba bmn Mesh Seed Msida apan ip e pu update Math jj Ter Lee T El Smooth ERR Thnk mm E A dake Smooth Meth A Tiree reads Manual Fant kin To gareraie dienple shin object i Set thee bounds for the skin bhert by dragsging the edges af Fhe green bow ga 162 lenges 2 Set the chresheed cordrols i9 f lert the ar pace around the LEGE Seger Update 4 N needed move the ised by maing the cursor and click fh Smooth Image Date Fl Mace Smooth Meah B Segmentation Tool Threshold window A Manual segmentation controls B Fast skin controls The threshold controls on the left side allow you to set the range of intensity values within the volume you wish to select The threshold opacity and colour allow you to set the colour and 68 Brainsight 1 7 E opacity of the selection to allow you to see the selection as well as the underlying image data The Smooth Image Data function allows you to smooth the images to obtain a surface with a smoother appearance It is rec ommended when generating skin and or skull surfaces The Make Smooth Mesh employs an improved algorithm to
72. essecceceecseeeeueeueeueuaues Calibrate the TMS Coil rarnrnnnnnnnnnrnnnnvnnnnernenennnnnn FOLLOWING THE CALIBRATE COIL TASK ASSISTANT Prepare the Brainsight Environment ccceceeee Chapter 1 Transfer Images to the Brainsight Computer Prepare the Brainsight Images Folder ce000 Direct DICOM Transfer ccccccsecceeeeceeeeeeeeeeeeseeees File Transfer Protocol ccccsccecceeeceeeeeeeeeeeeeeeeeees USING FTP TO TRANSFER FILES sssceceseeeeeeeeeeeeeeeeeeeees USING THE FINDER FOR FTP arnunnnnunnnnnnnnnnennnnnennnneennnnsnnnn Copy Files from an External Disk rrrnnrnnnrrnnrrnnnnnnn About Storage Media arannnnnnnnnnnnennnrnnnnnrnnevnnennnen Contents vii EE COPYING FILES TO THE BRAINSIGHT COMPUTER auunnnnnnnnnnnn 23 Chapter Preparing a Brainsight Project 25 Reload a Project cccccceccseeceeceeeceeceeceeeeeeeesseeeaaees 25 Brainsight 1 5 or Earlier Projects rrarennnenerr 26 Creating a New Project ccccsecccsseeeeeeeeeeeeeaeesaeees 27 LOADING ANATOMICAL IMAGES 0ccececceceeceeeececeeseeeeess 28 Functional Images rrarnnnrnnrnnnnnernnrnnnennrnnnnnnennnnnsen 28 OVERLAYING FUNCTIONAL IMAGES 0cceceececeeceeseceeeeeees 28 Save the Projelerine sensio 29 Prepare the Project for the Study r rrrrnnrnarnrannnnnnnr 30 Perform a 3D Reconstruction rrrarrarrernrrrrnvrnrnnnn 30 CREA
73. ever some subtle yet important differences If the functional data you imported in the previous section was the same size and orientation as the anatomical data then it 1s eligible for overlay on the anatomical data OVERLAYING FUNCTIONAL IMAGES You can activate the overlay by performing the following steps l Select the functional data in the Overlay pop up menu at the bottom left of the display window Figure 5 5 2 Select the functional image overlay in the Main Data Set pop up above the image Brightness Contrast thresh Chapter 29 Et old controls and set the threshold values The window should appear as in Figure 5 6 3 Set the overlay to the desired opacity by manipulating the slider in the overlay controls Figure 5 6 mr Ph 3 s a age ane Teaver rpa EE Oe p if fall rel enn ae dl bani 12538 Y Gr E FDOM Weed i 3238 FADE E 113 nr Screen shot showing functional image data superimposed on anatomical data The functional data can be seen on any 2D view as well as the curvi linear view Save the Project After the data loads save the project The project file saves the state of the software essentially a snapshot of all that is go ing on including loaded images open windows control settings and loaded data sets The first time you save a project go to either File gt Save or File gt Save As You can choose Save As at any time to create a project clone or create a project templa
74. ew window including some other windows in Brainsight for example Polaris Control Manual Trajectory any Task Assistant Rapid Fire Threshold If you close the Volume View the images and project data stay loaded in the Data Groups window Save Project saves the project as a Brainsight file Make sure you retain the file extension bproj when you choose a name Save Project As saves a project with a new file name You can use this any time you want to create a template for other projects a clone of the current project or change the name of the project for current and future saves Page Setup configures your printer preferences for when you use the Print View on page 50 button in either the 2D Mode or 3D Mode The only printing available is at the individual image pane 44 Brainsight 1 7 Er Edit Undo Cut Copy Paste Delete and Select All are stand ard software functions They can be used only when you work within text fields in Brainsight with the exception of the Seg mentation tool which supports Undo in a limited fashion See Segmentation Tool on page 66 for more details Window Data Groups brings the Data Groups window to the front It lists the images which have been opened in the current Brain sight project If you double click on a data set in the list or click on it then click on View a new Volume View opens displaying that data The Data Groups window cannot be closed Electrode Recordin
75. expected problem arising after the subject has arrived Arrange the Setup The Polaris optical position sensor used with Brainsight requires an unobstructed line of sight of the trackers on the coil pointer and subject Achieving this while allowing free move ment around the subject requires planning as there are three locations to keep in mind Il the camera location 2 the location and orientation of the subject tracker 3 the location and orientation of the coil tracker Generally the best location for the Polaris 1s above the sub ject s head looking down Figure 3 1 This allows the Polaris to see the entire area surrounding the subject s head while mini mizing the chances that you would have to stand between the camera and a tracker while performing the experiment Figure 3 1 is an illustration of a good setup for an experiment where the subject is sitting upright The Polaris is high mounted on the ceiling and pointing down on the subject s head This arrangement allows you to access the anatomical landmarks for registration and allows for movement of a TMS coil around the head Note that the Polaris Vicra has a different field of view In general it is a bit smaller but can also be put closer to the subject s head optimum 1m simplifying the setup in many situ ations DETERMINING THE CAMERA LOCATION Prior to beginning this procedure plug in and turn on in that order only the Polaris optical posit
76. g T nuts and slide the horizontal cross bar down the vertical bars until the bar is about 30 cm from the lower cross bar Make sure the cross bar is level by ensuring that the bar is the same distance from the cross bar at both ends Tighten the T nuts to secure the horizontal cross bar in place Place the 4 rubber stops Figure 10 6 on the vertical bars two per bar by loosening the T nut on each and slide them down the inside faces of the vertical bars Tighten them at the desired height The rubber stops prevent accidental sliding of the horizontal accessory bar down to the horizontal cross brace The height of the bumpers should be set low enough to not interfere with the movement of the horizontal accessory bar Set up the horizontal accessory bar Set the horizontal accessory bar onto the frame just enough for it to be stable on the frame but leave the ends of the bar exposed so that tools can be added Slide the TMS bar onto the exposed horizontal bar Place the square plastic bar ends onto the ends of the sliding accessory bar Slide the horizontal accessory bar down the frame until it is at the desired height Make sure the horizontal accessory bar can slide up and down reasonably well If it sticks particularly when raising the bar try loosening the T nuts in the middle horizontal cross bar and pulling the vertical bars slightly apart 1 2 mm and tightening them again Place all the plastic end caps on the
77. g is a simple utility to record and save the locations of EEG electrodes See Using Electrode Recording on page 54 for the procedure Electrode Recording for LOCATOR is an expanded version of Electrode Recording for electrode anatomical and head loca tions It can be used in conjunction with a sequence file in the Locator format for the order of the samples See Using Elec trode Recording for Locator on page 55 for the procedure Calibrate Coil is used to calibrate a TMS coil using the calibration block This is an automated software Task Assistant Manual Input is a tool that allows you to enter X Y and Z coordinates and the orientation of the pointer essentially to simulate the Polaris position sensor You can set the cursor posi tion using the Manual window 1 2 n depending on how many are displayed as the Input Mode in the Cursor Tool Polaris Control opens the Polaris Control window which al lows you to configure the Polaris optical position sensor helps position the subject and the tools and chooses the tool used on the subject Help View User Manual opens a screen resolution PDF version of this guide Red text is hyperlinked for ease of navigation Send Email to Rogue Research will open your default mail program and create a message addressed to support rogue research com Visit Web Discussion Forum opens your default browser at the support pages of the Rogue Research website Data Groups
78. gain using the corrected seed point If this does not yield a satisfactory skin object refer to Chapter 8 for more detailed instructions on performing manual seg mentation e g on noisy data Select Landmarks and Targets Select the landmarks in preparation for the subject image registration using the Marker tool refer to Marker Tool on page 63 Good landmarks must satisfy some guidelines First they must be unambiguously identifiable on both the subject and images Second they must be in the same location w r t brain at the time of the study as they were during the scan From our experience the best points to mark for registration are the bridge and tip of the nose and the notch above the tragus inter tragal notch of each ear These points can be selected by moving the cursor to the location on the 2D views see Figure 5 12 and using the Marker tool to record them The 3D skin object can also be used to verify the landmark locations identified on the 2D views or to select the landmarks directly on the 3D skin Figure 5 13 In the view where a 3D skin is being displayed bring up the list selector and select the Pointer sphere to represent the cursor location with a small blue sphere Select the 3D cursor tool for that view and click directly on the skin object to move the cursor to that point You should use the 2D and 3D views at the same time to take advantage of all the available information to select the best l
79. generate smoother and more accurate meshes It is disabled for non isotropic image data There are two methods for segmenting objects Manual and Fast Skin both are described in the typical usage section below MANUAL SEGMENTATION CONTROLS The manual method allows you to control each step of the segmentation while the fast skin method allows you to generate a skin segmentation with minimal interaction Choose the method by selecting it in the tabs along the top of the window In the manual mode you can select which segmentation tool to use e g Seed Area by selecting the button The selected tool will act when you click the mouse in the image view so the tool s description below applies when the tool is active and you click in the image view Seed Area default creates a seed object at the click location and then fills all areas connected to the seed whose intensities are within the threshold range similar to a paint bucket tool in a drawing program Moving the cursor to another slice will pull the seeds along with it and re apply the fill from those points to the new slice automatically e Add Line and Fill Region work together to manually fill a region delineated by structures which can be isolated or missed by using the Threshold range control Typically you add a line around a structure to delineate then select the fill region tool and click or stay in the add line tool and use the option click short
80. h 62 Brainsight 1 7 SSS eee If your mouse has a scroll wheel rotating it forwards and backwards has the same effect as Using the Up and down arrow keys Figure 8 3 Input Mode Manail 1 M Active 1 Tip Offset 3 00 Current Registration Brainsight to World New Manual Req New Assisted Req Import From File Di Closeup of the cursor tool s control pane A The tip offset slider and indicator B The registration popup menu allows you to manually set the coordinates and angles of a simu lated tool This window outputs these values and becomes avail able from the Input Mode pop up menu allowing you to enter coordinates to drive the display and the volume cursor The Distance to Marker box shows the distance between the current location of the cursor and both the selected marker from the Markers list in the Marker Tool control pane and the closest marker to the cursor Figure 8 3A shows a closeup of the controls highlighting the tool offset control This control allows you to add an offset from the currently tracked tool s tip along the tool s trajectory This makes it easy to project the cursor tip from the scalp into the head while tracking the pointer or TMS coil The visible hidden green red display will turn green amber to indicate that the cur rently tracked tool and subject tracker are visible but the amber is to remind you that the displayed tip is not the true tip locat
81. hat height of the two pins in front and in back of the centre pin are such that they support the coil during the calibration process At the prompt Figure 3 9 Step 4 place the coil in the calibration position the centre pin on the hot spot and click the Calibrate button After clicking Calibrate you have a five second countdown to give you time to ensure the coil is in the calibration position After the countdown the computer beeps once then monitors the coil location for another five seconds The computer beeps a second time indicating that the cali bration is complete If you are not going to prepare any studies you can quit Brainsight Prepare the Brainsight Environment If you want to use a project you created in another version of Brainsight you first need to set up your environment The project opens with all the states of the environment it was saved in which will not necessarily work with your new setup To set up your l LA environment do the following Make sure that you have set your Preferences Setting Preferences on page 10 including Polaris preferences Check that the Polaris on 20 Brainsight 1 7 E e Remember that your coil calibrations need to be stored in the Tools folder 3 Open Brainsight and select Window gt Polaris Control to see if the software can communicate with the Polaris you should hear the characteristic 2 beeps and that the pointer
82. he Polaris the next time you load the project again unless you want it to Save the Project If during the TMS sessoin you have recorded new markers and trajectories remember to save the project to record the ses sion to disk Export Images and Movies If you need a still picture from Brainsight click the hard disk icon in either the 2D or 3D view of any Image View pane 42 Brainsight 1 7 me Figure 6 10 Filename Untitled mov Frame number 0 This function allows you to link a view to a QuickTime movie to save a dynamic view of your images Every time the view is updated in any way a new frame is added to the movie of your images Clicking the Export to QuickTime button causes Brainsight to prompt you for a file name and then the record ing control window appears Figure 6 7 To record the movie Brainsight appends an image each time the view window re freshes Click the rectangular Stop button to save the movie to the file name Chapter I Software Reference Figure 7 1 MINC THM NEMA DICOM Philips ANI V N Analyze NIfTI hdr amp nii V A Import Images menu Brainsight does not have a file gt Open Recent Projects gt menu Brainsight can only have one project open at a time If you want to view or open a recently used project use the Apple gt Recent Items menu Brainsight projects are in the Documents section of this menu se this chap
83. he desired orientation Use the Curvature slider to project the grid to the curved surface e If you are planning to create a series of trajectories use the trajectory twist angle to orient the trajectories in the desired orientation the orientation you will want to have the coil be at for stimulation e If the grid is where you want it click either the Copy to Markers or Copy to Trajectories to create a series of markers or trajectories for each node of the grid e Select the Marker or the Trajectory tool to confirm that the grid was copied to the appropriate list e Use the Markers or Trajectories during your normal TMS session DETAILED STEPS Step 1 Use the segmentation tool to create a 3D skin object or use the curvilinear reconstruction tool to create a 3D cur vilinear surface The easiest way to place and orient a grid is to have a 3D surface to select the location When you use the 3D cursor tool 16 Brainsight 1 7 N to click on a skin or curvilinear reconstruction the position of the cursor is set to the location of the click The orientation as observed with the inline and inline 90 views and by the trajec tory stick object in the 3D view is also set to the normal of the surface at the location of the click One can use the skin or brain as the location for the grid Us ing the brain has advantages the main one being that the targets will be cortical targets rather than scalp targets Using
84. he rear foot such that the slots of the vertical bar go onto the T nuts of the foot You may need to loosen one of the A Front foot corner brackets to get it to fit and you may need to align the T nuts for them to enter the slots Watch out for your fingers Once the T nuts are aligned the bar may fall into place quickly pinching your fingers in the process Figure 10 16 B Rear foot Assembled main frame 94 Brainsight 1 7 Figure 10 17 6 Slider block Figure 10 18 Add the slider block for the chair by loosening its lever and sliding it onto the and of the horizontal bar Figure 10 17 Place the coil rail assembly onto the vertical bar First loosen the T nuts that will be going into the vertical bar These consist of the 4 middle nuts of the front plate and 3 pairs of T nuts inside L brackets one at the rear and 2 on the lower sides as shown in figure 10 18 It may also help to loosen one side of the nuts holding the bracket together e g 2 of the nuts on one side of the front plate to give the assembly more play Next lift the assembly over the verti cal post and while keeping the T nuts aligned so they don t twist and bind rather than enter the slot lower the assembly into the post Stop when the top of the assembly Loosen these nuts circled in red before inserting into the vertical bar Figure 10 19 g 9 10 Forehead rest mounting plate is flush with the top of the ver
85. his text referring to a tool usually means referring to a tool and tracker pair that is coil tool refers to a tracked TMS coil The tool is tracked by either designing it with a tracker built into it such as the pointer or has a tracker attached to it such as the TMS coil The position reported is the location of a point defined as the tool s origin In the case of the pointer the origin is the tip of the pointer The tool s orientation is the orientation of a prominent axis of the tool Again in the case of a pointer the orientation axis Is the orientation of the pointer s shaft In the case of a coil tool the orientation is the axis of the magnetic field of the TMS coil Refer to Chapter 8 for a discussion of software tools Software Terms The software is described in detail in Chapter 7 Software Reference However the following items are described here as they are necessary components to calibrate your Brainsight installation TOOL CALIBRATION FILE Brainsight requires a tool calibration file to relate the tool to its associated tracker for example a coil tracker attached to TMS coil The pointer and the subject tracker come with their own calibration files while calibration files for the TMS coil tool are created when it is calibrated by the user refer to Cali brate the TMS Coil on page 16 TRACKER CHARACTERIZATION FILE ROM FILE The Polaris needs to recognize the expected dimensions
86. ick the Convert to marker button the window in Figure 8 9 appears Enter a unique Prefix and the Offset dis tance along the trajectory for the markers you want to create and click OK Figure 8 9 Convert Trajectories to Markers This utility converts all recorded trajectories Into new markers You have the option of l Adding a prefix t the trajectory name when converting to markers 2 Adding a fixed offset along the trajectory path from Its origin Prefix Offset fram origin 0 00 mm Ottsatsl Citsetall Convert to Markers window Segmentation Tool General Description The Segmentation tool is used for segmenting volumes to measure the volume of certain anatomical structures for ex ample the hippocampus It can also be used to render surfaces for structures for example you can render a skin surface of the subjects head skin segmentation Figure 8 10 Tools Volume ohjects Fd pebete a F gd Overlay opacity Display All f show volumes Segmentation Tool control pane Figure 8 11 New Segmented Object Label Volume 1 E Tr naverse 4 Calaur Doacity Direction New Volume input window Use the Opacity slider with cvaution as the resulting translucent volume may result in slow display performance Figure 8 12 Veluria Volume in cubet millimeted oluene 1 S24 mms Show Volumes dialog Chapter 8 bl DoT A surface i
87. ift clicking the first and the last in the list this should highlight all files and click the Open button Brainsight scans all the selected files to sort the individual slices during the loading sequence If more than one sequence was selected a dialog appears requesting that you select the desired sequence The following are the file types to look for e MINC requires mnc files e Analyze requires hdr and img files e NIfTI images can be either hdr img pairs or nii 28 Brainsight 1 7 CLI If you choose Manual remember that your image data could be 8 15 or 32 bit but the actual minimum and maximum voxel values are only a portion of each corresponding range I to 28 216 or 232 Figure 5 4 Image Data Mapping Linear CT Brain Pixel Mapping Style v MR Brain MR Brain 2 ce MR Brain 3 1 Manual Select Image Dati Mapping Style Figure 5 5 Overlay Data Brightness Contrast Threshold 10 9 0 00 Overlay i fmri res mnc Opacity 2D view zoom m Image manipulation panel e DICOM has no official extension specification but dcm or ima are often encountered LOADING ANATOMICAL IMAGES Il Launch Brainsight 2 Select File gt Import Images gt example format and select the images mnc hdr ni1 or multiple files and types corresponding to the anatomical data set 3 If your anatomical data uses 16 or 32 bit integers a second dialog
88. ile Egg hF ara Mente HH saler Cear Image Main ace tet PF er E A i braga rae cera et me BD ve ajala EG 0 00 ajej OM M les Image Controls je 4 Cear 4 _ Brainsight X 67 00 Y 141 00 180 00 World eq Ai L83 Y 1321 2 5 74 fin mm Volume View window Volume View Window You can only see this window by importing some images Go to File gt Import Images gt MINC and choose roch mri corrected mnc from the Sample Data folder copied to your hard drive from the Brainsight CD After the images load the Volume View window appears Figure 7 5 It holds six in dependent Image View panes a Tool Bar a Tool Controls pane and an Image Controls pane The title bar of a Brainsight Volume View has the following format lt name of the data set gt n n is equal to 1 2 3 or any other number depending on how many view windows have been opened of that data set since the beginning of the Brainsight session e The Image Controls allow you to change cosmetic pa rameters of the images like the zoom and the Brightness Contrast threshold level of the data displayed When functional data are displayed statistical maps and the file is a floating point format the numbers shown on the controls correspond to the actual data Chapter 49 3 Figure 7 6 values allowing you to easily set the threshold for the display View Mode Selector Image View panes contain
89. ilinear surface you created and named are checked off Click OK The 3D image pane updates to display the curvilin ear reconstruction 14 Use the Peel depth slider in the Curvilinear Tool control panel to navigate the 3D reconstruction Add a Skin Segmentation This section is optional however it is a way to model the sub ject s face in order to simplify the task of identifying the land marks reaquired to register the subject to his or her MRI For details of the tool options and dialogs see Segmentation Tool on page 66 The segmentation tool functions in two modes The manual mode which allows you to control each step of the segmentation process and the fast skin mode designed to segment the skin with minimal work For this tutorial the fast skin method will be used Refer to Chapter 8 for more details regarding segmenta t10n CREATING A SKIN SEGMENTATION 1 Choose the Segmentation Tool 2 Click New to create a segmentation volume Enter the information in the screen Figure 5 8 You can edit the name of the volume and the colour or accept the default Select the orientation you wish to work in however Transverse is usually the best orientation Once the in formation has been entered click OK The Threshold window appears Ensure that the Fast Skin tab is selected Pull the upper threshold down to remove the purple threshold colour from the MRI data that is select the background and not the im
90. ion 7 Inthe Manual Trajectory window enter the X Y and Z coordinates you obtained from your analysis software for that same landmark Click on the Sample button in the Registration Tool window You should see a registration entry with the coordinates you entered as one set of X Y and Z coordinates 8 Repeat steps 6 and 7 for all the anatomical points you identified 9 When that is done press Apply in the Registration Tool window and save and apply registration Note that the registration will be listed as Foreign in the registration popup menu 10 In the Cursor tool select Manual as the Input Mode Then select Active just as you would for the pointer tool Now enter the X Y and Z coordinates of any tar get from your analysis software into the Manual Trajec tory window The cursor should go to the homologous spot in Brainsight ll As an additional check move the cursor to various brain locations in Brainsight and confirm that the coordinates displayed in the Manual Trajectory window agree with those of your analysis software at the same location If they do not agree a An error was made in the registration process Or b The images in your analysis software were normalized In case of a change the pointer input back to mouse delete the registration points in the registration window and repeat the registration procedure steps 5 11 In case of b use the original non normalized images
91. ion but the projected location using the offset value from the slider The popup menu at the bottom of the control pane Figure 8 3B allows you to select the current registration that is applied to map external coordinates e g the pointer to the underlying Brainsight s image coordinates For example after performing a subject to image registration the Subject to brainsight reg istration is used to map the pointer coordinates to Brainsight s coordinate system The menu allows you to select any pre exist ing registration or to initiate a Subject Registration by selecting either New Manual Reg for the manual registration or New Assisted Reg using the task assistant Typical Usage Notes Use the Cursor tool to initiate a subject image registration by choosing New Assisted Reg from registration pop up menu When the Cursor tool is active you can click the mouse on any 2D view to move the volume cursor to that point The posi tion of the cursor 1s shown by the cross hairs in each 2D view To use the arrow keys or the mouse s scroll wheel if one is present to move the cursor place the mouse over any of the 2D views and strike either the up or down arrow keys This causes the cursor to move into and out of the plane of that view by steps of one millimetre or any other value set in the General Prefer ences For example place the cursor over the sagittal view and press the up arrow key The curs
92. ion sensor in order to give it time to warm up The standard Polaris requires up to 30 minutes while the Vicra requires up to 10 A good way to evaluate a proposed setup is to use the pointer and the Position Camera function in Brainsight see Figure 7 4 To use this tool set the camera location and experimental setup to your proposed setup and perform the following steps Il Launch Brainsight 2 Make sure the Polaris is connected to the workstation and that it is on Select Window gt Polaris Control for more information see Polaris Control Window on page 45 Note that your pointer and subject tracker should appear in the list of tools in the window If the list is empty make sure that the default tools folder prefer 14 Brainsight 1 7 SSS Figure 3 2 A B Two methods of attaching a tracker to monitor head movement A Head strap B Glasses Figure 3 3 gt HexRod Collar Set Screw Close up of a hex rod and collar ence is correctly set see Brainsight first run in Chapter 2 3 Select a tool to view such as the Pointer by selecting it from the list of tools First Run If this is the first time you are using Brain sight please verify that the pointer and subject tracker files both calibration and ROM files agree with the tool serial numbers If they do not match contact Rogue Research before proceeding 4 Ifthe Polaris is not already tracking as seen by the red or green box indicating th
93. ion size 3 00 mm JD annotation size 3 00 mm ID rendertype Onsecreen Slice Increment size 100 mim 2D annotation display sensivity 100 mim Imaging convention L R R L Radiology C L L R Check for new Grainsight release Weekly E Check Now General Preferences dialog 7 In the General pane select the colours you prefer for the 3D rendering background cursor and annotation colours 3D Render type refers to performing the rendering On screen which is faster but can be limited by the VRAM on your graphics card or Offscreen which is slower but more reliable Select Onscreen Unless you are using an older Macintosh e g has a graphics card with less than 64MB of VRAM you should select Onscreeen render ing If the textures within the 3D views look abnormal random noise instead of an MRI switch to Offscreen mode Slice increment refers to the step size when using the ar row keys or the mouse scroll wheel with the Cursor tool to move the cursor You can also set the imaging convention between screen left subject left or screen left subject right Radiol ogy convention facing the subject The subject right is always labelled with the R indicator on the screen In the Default File Paths pane Figure 2 7 select the default directories for your images These defaults act as starting points to find your images for the correspond ing File gt Import Images menu commands Also set the Tool
94. k OK Select the Curvilinear tool select the surface family in the list shown in the tool control pane Slide the Peel depth slider to choose the offset to view Select the Marker tool then select your target from the list of markers by clicking on it in the list Set two other 2D view panes to Inline and Inline 90 You can also use the targeting tool In one of the 2D views select Marker Targeting This brings up a bull s eye view of the target from the coil s perspective see Figures 6 5 and 6 6 Figure 6 5 Car amu TAa amp Illustration of a TMS coil seen from above The red cross hair illustrates the hot spot of the coil identified when the coil was calibrated and also the Bull s eye view The black dot represents the target To line up the dot with the cross hair move the coil in the direction of the arrows represented in the coil s view Chapter 6 39 3 7 Select the Cursor tool and set the Input Mode as Coil Brainsight uses the coil input to drive the display 8 As you move the coil close to the target you can see all the views in the window continuously update according to the coil location The bull s eye view shows the distance from the target to the coil s projected axis e g the centreline of the calibrated hot spot A value of 0 means that the coil is pointing directly at the target Figure 6 6 During a targeting task you can use the 3D views the inline views and the b
95. ker is the head strap It 1s a simple elastic strap with Velcro ends allowing it to fit snugly and comfortably on any head There is a small flat pad that rests on the head to stabilize the hex rod collar connected to the tracker itself See Figure 3 3 If the subject is wearing electroencephalograph EEG elec trodes the strap can obscure them In this case use the tracker glasses Tracker glasses consist of a pair of safety glasses with hex collars mounted on either side of the frame The glasses arms and frame can limit access to frontal areas of the brain In that case the head strap would be more suitable In cases where attaching a tracker to the head is impossible use the forehead rest mount for the subject tracker This method is the least accurate The forehead rest of the head and coil holder which has two hex rod mounting points does not track the head directly It can be used in cases where you are confi dent of head stability during the experiment while allowing for movement of the camera without loss of registration Reflector Spheres Trackers use reflector spheres that are visible to the Pola ris camera These spheres are connected to special posts The spheres are fragile and sensitive to dirt Any physical damage or dirt on the spheres can affect the accuracy of the tracker There fore avoid touching the spheres directly with your hands as the oils can harm the reflective surface Use a lint free cloth or
96. l the connections are made power up the Polaris Use the On Off switch on the Polaris box This is on the back panel 8 Brainsight 1 7 E Do not use a USB port on the keyboard as it may not provide enough power to the adapter such that intermittent problems may occur Figure 2 3 To Computer USB Port Viera Power Supp To AC Power via Surge Suppressor Figure 2 3 Polaris Vicra wiring diagram of the cart if you have the turnkey system The main power switch of the cart must be On POALRIS VICRA Before connecting the Vicra for the first time run the Vicra driver installer found on the Brainsight CD or disk image de scribed in the next section The driver should be named Polaris Vicra FTDI USB Serial Driver or something similar The Vicra has one cable conected to it which provides both communications and power Figure 2 3 At the other end a small dongle has a USB connector to connect to the Macintosh computer and a power connector to connect to the included pow er supply Note that the dongle contains a USB Serial adapter similar to that used with a standard Polaris so when the manual refers to a USB serial adapter it also refers to the dongle Connect one end of the cable to the Vicra Connect the USB cable to the dongle at one end and to a USB port on the compu ter or powered USB hub connected to the computer at the other end Do not connect it to a USB port on the keyboard as this will yi
97. lace the L brackets on one leg first call one bracket the rear one and the other the front one Use the first leg as a template for the second leg to ensure that they Figure 10 2 are at the same position along the horizontal bar See Figure 10 2 3 Attach the vertical bars to the horizontal legs a Fix the diagonal braces to the vertical bars so they look like the base in Figure 10 3 b Carefully slide each vertical bar on to the horizontal legs you may have to adjust the T nuts on the bottoms of the vertical bar c Make sure that they are aligned with the L brackets on the horizontal bar Tighten the nuts in the vertical bar and diagonal braces so the vertical bar is fixed firmly Figure 10 4 shows the finished side of the base in L ith L bracket l p ae preparation for connecting the left and right sides with a horizontal bar Figure 10 3 Fiaure 10 4 Base of head holder frame left side and horizontal bar belonging to base 4 Attach the horizontal base to the horizontal legs assem bled above a Loosen the T nuts on the L brackets on both left and right sides of the base b Slide the base bracket into the ends of the left and right sides c Tighten the T nuts again 5 Assemble the basic frame See Figure 10 5 Base with brace and vertical bar a b c Figure 10 5 d a b c d Horizontal bar Figure 10 6 Rubber stops Chapter 10 89 E Loosen the remainin
98. ll points heave been siler m Skip Point gt Sampla Pip Foint 3 Press Go To Previous Point to rsample the peceding point 4 sa Lo 10 Previous Point H Pointer visible Step Info Subject visible Once you have sampled all the paints press Go To Next Step G to Previous Step Go to Next Sten Step 3 If either the pointer or subject tracker is not visible to the Polaris its indicator in the step window will be red and the Sample Point button wil be greyed out disabled Move the tools into the field of view to enable the Sam ple Point button If either box remains red no matter where you move the tools you may have a Polaris problem See Determin ing the Camera Location in Chapter 3 or contact Rogue Research to arange to have the camera tested and or serviced Brainsight automatically brings the cursor on the screen to the first landmark marker recorded earlier If this loca tion corresponds to a registration point not a target bring the pointer to that point and click Sample Point otherwise click Skip Point to proceed to the next marker on the list without sampling it The Task Assistant cycles through all the markers in the list which you identified earlier When all the registra tion points have been sampled click Go To Next Step Figure 6 4 appears 38 Brainsight 1 7 N Figure 6 4 b Tasi Assistant Begs i Step 4 Verify Registration Finally move the poin
99. ls the position of the 3D volume cursor which in turn controls the slice displayed in each of the 2D views in the Volume View window There are three basic ways of moving the cursor location using the mouse using the scroll wheel or using arrow keys on your keyboard However there are other inputs through the control pane Control Pane Description For the Cursor tool control pane refer to Figure 8 2 When the Polaris is in use and a subject image registration has been performed you can select from the following Input Modes to act as input to drive the display Mouse Pointer Coil Subject appears in the list however there are no meaning ful instances where you would select it If the manual trajectory window is open it also appears in the Input Mode menu The behaviour of the mouse has two settings Live enabled and Live disabled When in Live mode the cursor updates con tinuously with the movement of the mouse while the button is held down click drag action When not in Live mode the cursor updates only when the mouse button is released Subject Pointer and Coil are available from the Input Mode pop up menu if the Polaris Control window is open and tracking Then you can enable or disable the Active checkbox to freeze the display To move the cursor using manual coordinates you first have to select the Window gt Manual Input menu This menu is available at all times and brings up the Manual window whic
100. m the target to the bull s eye plane NOT taking the trajectory into account The resulting display is a cross hair representing the coil s center a circle representing the trajectory scalp entry and finally the dot for the target The best way to use this display is to remember two steps First move the coil laterally towards the green circle until it is in the middle at the scalp entry point Second tilt the coil until the black dot is in the middle Finally the twist can be adjusted until the green tab like a minute hand in a clock is pointing up Record Location of Coil You can record the coil position using the Trajectory tool Select the tool in the tool bar and when you wish to record the coil location click New in the tool control pane Enter a name for the trajectory For more information see Trajectory Tool on page 65 If you are recording more than one location you can use the Rapid Fire feature Proceed to the next section Rapid Fire Configuration and Operation A Place the coil near the target B Translate the If you wish to record multiple coil locations rapidly click on coil towards the green circle C Tilt the coil until the Rapid Fire button in the Trajectory tool control pane this the dot is in the middle D Twist the coil until the also works with the Marker tool The Rapid Fire tool enables green tab is pointing up you to record multiple coil locations with a minimum of interac tion With
101. mera Polaris Control window Tracking These buttons command the Polaris to start and stop track ing When ON the Polaris begins tracking and sends data to the computer Reference Frame This menu sets the tool used as the reference tool That is all other tool locations will be calculated with respect to this refer ence tool If Brainsight has not automatically loaded the subject tracker as a tool check your preferences See Errors and Trou bleshooting on page 58 Because the reference tool 1s normally set to the subject tracker all tool coordinates pointer and coil tool are calculated with respect to the subject tracker This allows you to move the camera without losing the subject image registration If the sub ject tracker is being worn by the subject not on the head holder the subject s head can move without loss of registration as long as the subject tracker moves with the head If the subject tracker moves with respect to the head for example it gets shifted or bumped then you must re register the subject Tools List and Controls This list shows the tools currently loaded into the Polaris Clicking on one of the tools selects it and detailed information regarding that tool is displayed below the list Clicking on the Add button brings up a dialog box to allow you to select a tool to load into the Polaris Select a coil calibration file to load a coil calibration you may have creat
102. n the Add Line Fill Region and Clear Line Clear Region tools to delineate the objects slice by slice 1 Choose the Segmentation Tool 2 Click New to create a segmentation volume You can edit the name of the volume and the colour or accept the default Decide on the orientation in which you wish to work in in delineating the structure of interest 3 The Threshold window appears Select the manual tab 10 Brainsight 1 7 SSS Se Figure 8 14 ees gt Thresholded Seed Applied Add Line Fill Region Illustration of adding a region using the add line 7 Fill region tools Figure 8 15 e s lt its 8 9 Thresholded Seed Applied Q Draw Clear Line Clear Fill Region Illustration of clearing a region using the clear line clear region tools 11 12 13 Move the cursor to the slice in which you want to start Verify that the threshold highlights the desired structure select Seed Area and drop a seed in the highlighted area see figure 8 13 Note that the seed will apply a fill starting at the seed point using the intensity range displayed by the threshold colour Choose the seed loca tion keeping in mind that as you move to other slices the seed will follow to these slices Choosing a location where the structure will likely be in the next slice will increase the chance that the seed will land on the desired structure again Add more seeds as required to select all
103. n this document to be l 2 3 4 5 Comments I found the procedures in this document to be l 2 3 4 5 Comments I found the illustrations and examples in this document to be l 2 3 4 5 Comments I found the publication quality of this document to be l 2 3 4 5 Comments Feedback 103 Er After using this document I have a better understanding of the product True False In future versions of this document and related documents I would like to see the following document organization changes of format or content or new topics Comments Brain Q GESEARCH Inc pt Research Inc 4398 Boul St Laurent 206 Montreal OC H2W 15 Phone 514 284 3888 Toll Free North America 1 866 984 3888 Fax 514 284 6750 http www roque research com
104. ndle ring is usually fixed per manently onto a coil therefore if you have more than one coil you can buy one for each coil Two screws hold the ring halves together in place on the handle One tracker can be used with many coils The hex rod 1s used to attach a tracker to the handle The hex rod and tracker can be removed and fixed to a coil handle ring quickly so you can eas ily move the tracker from coil to coil You can also vary the position orientation of the hex rod at either end This enables you to orient the tracker to face the posi tion sensor camera when the coil is in the stimulating position over the subject Subject Tracker The subject tracker allows the Brainsight system to monitor the position of the head by attaching a tracker to it By tracking the head Brainsight can make it the reference for all other tools such as pointer and coil tracker These tools can be localized in the head s coordinate space rather than the camera This has two benefits The system detects and shows both coil movement and head movement both of which can cause you to miss the target e The position sensor camera can be moved without loss of the registration from the subject to the images This is important if adjustments to the setup are required after the registration Chapter 9 83 There is more than one way to attach the tracker to the head to accommodate different experimental setups The most common subject trac
105. ne The following are useful tips for adjusting or removing guide Curves Move any guide curve control point on the curve by click dragging it to the desired location To remove a point on the curve click to highlight it in red and press the Delete key Also if you click the mouse between two 4 Brainsight 1 7 E Figure 8 23 Example of a grid over the motor cortex and sur rounding area points a new control point is inserted in between the two points e To edit a curve click the desired guide curve indicator This brings you to the corresponding MRI slice that you wish to edit Note with multiple windows open only one will allow you to edit a surface e If you go to a slice between guide curves the software displays where the surfaces intersect that slice by dis playing dark green curves on that slice This indicates how well the interpolated surface conforms to the actual surface at that slice If as you add more guide curves the interpolated curves conform to the surface you want you need not add more If the interpolated curves do not conform well to the surface add a new guide curve e To change the offset values after you have begun drawing the surfaces select the surface family in the list located in the Tool Control panel Once selected click Edit to display the Curvilinear Surface Family Preferences win dow Figure 8 18 Make changes to the offset values e If you create a surface f
106. ntation is correct you can rotate the grid about its central axis to optimize coverage over your area of interest Fig 8 30 illustrates this Figure 8 30 Illustration of using the Twist slider to rotate the grid about its center Step 8 Use the Curvature slider to project the grid to the curved surface So far the shape of the grid is flat You can approximate the curvature of the surface by adjusting the curvature value The curvature 1s spherical in nature so it only approximates the curvature of your surface Choose the curvature value that best approximates the surface fig 8 31 Note that the normals of the trajectories also spread out according to the curvature fig8 32 Figure 8 33 The twist slider allows you to twist each trajectory about their respective axes FY The twist can be used to set the twist angle of the TMS coil using the trajectory targetting assistant Chapter 8 19 TT Figure 8 31 Curvature adjustment using the Curvature slider Figure 8 32 Adjusting the curvature also adjusts the normals of the trajectories In creasing the curvature spreads the orientations out in a spherical manner Step 9 Set the trajectories twist angles When using trajectories for targeting you can make use of the twist angle in addition to the position and orientation review the operation of the trajectory targeting view page 40 You can set this angle by using the twist angle slider Note h
107. of a tracker in order for it to track it This information is kept in a description file and can be recognized by the ROM extension Each tracker comes with a ROM file whose file name usually matches the serial or part number of the tracker itself 4 Brainsight 1 7 3 POLARIS CONTROL WINDOW When the Polaris is connected to the computer you can control its functions within Brainsight using the Polaris Con trol window Among other things it enables you to configure the tools and trackers you are using as well as start and stop tracking This will be covered in more depth in Polaris Control Window on page 45 What s New List of Upgrades The Brainsight features in this section are new or have been upgraded in v1 7 Automatic Update Notification If your Brainsight computer connects to the Internet you can now check for product updates through the Preferences window or set the time frame for automatic updates If at Brainsight start up a new version 1s found the following dialog appears Figure 1 4 There is a newer version of Brainsight available _ You are using version 1 d4 and version 1 7d5 is now available C Ignore Update Update dialog If you check for the product update and your version is up to date the following dialog appears Figure 1 5 No newer version of Brainsight is available SAR You are already using version 1 7d5 which is the latest No update required
108. ol Pane Description Grids are created edited and deleted by clicking on the New Edit and Delete buttons respectively Like the Marker and Trajectory tools the 2D display of the nodes and their labels are controlled by the Display in 2D and Display Labels checkboxes If the Perisitent Display checkbox 1s tog gled the grid will be displayed regardless of the current tool Toggling it off will hide any created grids when other tools e g cursor Marker tools are selected TypicAL Usace Notes The grid tool is usually used to create an array of markers or trajectories by following these steps Use the segmentation tool to create a 3D skin object see page 66 or use the curvilinear reconstruction tool to cre ate a 3D curvilinear surface e Configure a 3D view to see the surface and a representa tion of the cursor e g cursor sphere or trajectory stick Configure 2 of the 2D views to display the inline and inline 90 views Use the 3D cursor tool to select the centre spot where you wish to place a grid Select the grid tool and create a grid by clicking New in the tools control pane Set name the number of rows and columns as well as the spacing between the rows and columns e Use the AP and Lat angle sliders to tweak the overall an gles of the grid to ensure that it is normal to the surface Use the twist angle slider to rotate the grid until you have t
109. ol points into the sulci but rather create an outline of the overall curvature of the brain roughly along the dura as shown in Figure 5 7 amp Figure 5 8 New Segmented Object Label Skin Colour Opacity IIl To Direction Transverse Cancel Data entry screen for creating a segmented object Chapter 3 EE 10 Click in another orientation you no longer need to com mand click as you did in previous versions of Brainsight or use your mouse s scroll wheel to change the location of the cursor and return to the selected orientation to start a new guide curve There are no arbitrary rules as to the spacing of the guide curves you are free to decide how to space them However it helps to have one guide curve in the middle of the brain and one at each extremity in the plane of your choice Then add new guide curves between pairs of existing guide curves to subdivide the sections between them until the interpolated curves agree sufficiently with the actual brain outline 11 Start a new guide curve as you did in step 9 Repeat steps 9 and 10 at least three times with guide curve indi cators well spaced The more guide curves the better the representation 12 To view the 3D reconstruction in a 3D view click the 3D mode button in an image view pane click the 3D Object Selection button see page 52 13 Scroll through the list and make sure that the curv
110. ompletely defined over the entire surface of the brain For example when using the coronal plane to the draw curves the resulting reconstruction will have well defined temporal and parietal lobes but the poles of the frontal and occipital lobes are omitted In contrast if the sagittal plane is used to draw the curves the frontal and occipital lobes will be well defined but Curvilinear surfaces derived from guide curves the poles of the temporal lobes are omitted Examples of recon drawn in the sagittal lefi and coronal righ structions using the sagittal and coronal planes are shown in planes Note that in the sagittal derived surface Figure 8 16 the temporal lobes are not represented while the coronal derived surface lacks anterior and poste Control Pane Description rior poles The control pane for the Curvilinear tool is shown in Fig ure 8 17 The Surface Families are the 3D surfaces you have created Figure 8 17 Each can be viewed as a 3D Object in a 3D view pane New and Edit bring up the Curvilinear Surface Family Preferences dialog Figure 8 18 to create or change a new or a selected surface family Delete discards the surface family IE Fel Cpaliny Fit rann rann nat Peeldepth gt EE M Edit Curves Progress Curvilinear tool control pane 12 Brainsight 1 7 LD E Figure 8 18 Figure 8 19 F rk es rlan Fama Bee seu Pr Beo arter ITE Baria Famy Type Ds Hi Jen
111. on of the Talairach coordinates which may have subtle dif ferences to the original Talairach and Tournoux atlas Place the subject tracker using the tracker glasses on the subject being careful not to disturb the EEG elec trodes In Brainsight open the Polaris window and set the track er status to ON Ensure that the Polaris is configured to track the pointer and subject This should be automatic Select Windows gt Electrode Recording for LOCATOR The window in Figure 7 15 appears Press Load Sequence and select the sequence file which is a file type that Locator uses See the Locator or BESA user manual for more details about the sequence file From the Pointer pop up menu choose Pointer Type the Subject Name According to the sequence given sample the electrode locations anatomical locations and locations on the sub ject s head using the sample button beneath each list If you made an error sampling a point delete the point by selecting it in the list and pressing the delete button Type the name of the electrode or anatomical landing in the Next sample test field and resample the point Press Save LOCATOR Save Opt3D or Save BESA any time you want to save data These three options are essentially variants of the Locator file format The underlying coordinate system has subtle differences 56 Brainsight 1 7 773 between these formats You may need to experiment and vali
112. or moves either deeper or more superficially through the image subject left right perpendicu lar to the sagittal plane While moving various objects for example cursor and mark ers you can constrain their movements to either the vertical or horizontal axis by holding down the shift key during movement You can use the Manual Input with Cursor Tool Input Mode set to Manual Active for instance to rapidly enter co ordinates for annotations that have been exported from a different time or project using the same subject s MRI data The accuracy of the measurement depends SF on the voxel size information in your image header being correct Perform a validation before making any measurements F igure 8 4 right ear left ear nose bridge i Mark Delete mn E Edit Rapid R Display in 2D Display labels d Export v Lock Marker tool control pane Chapter 8 63 I Ruler Tool General Description The Ruler tool provides an easy way to make measurements in any 2D view Control Pane Description The Ruler tool has no control pane objects Typical Usage Notes Activate the Ruler tool by clicking the button and click drag the mouse in any 2D view Clicking the mouse button down sets one end of the ruler to that point While holding the mouse but ton down drag it around While the button is down the other end of the ruler follows the mouse A line is displayed
113. ow the direction of the vectors change fig 8 33 The arrow at the base of the vec tor should point forward in the coil s perspective away from the handle Step 10 Use the grid template to finally create markers or trajectories for each grid node While the grid displays an array of trajectories it cannot be used as a sequence of targets yet The grid serves as a template to create a series of markers or targets Once you are satisfied with the grid you can use it to generate the markers or trajec tories If you want a sequence of markers click on Copy To Markers A marker will be created for each node in the grid The naming convention will be Grid Name row col where Grid Name is the name you entered for the grid 80 Brainsight 1 7 N Chapter 0 Hardware Reference Figure 9 1 Coil calibration block stabilizing pins his section describes the Brainsight TMS hardware and provides care instructions Hardware Components Tool Box The tool box for the non cart system typically includes e the pointer e two trackers coil and subject e coil handle ring prior to attachment to coil or other coil adapter e subject tracker glasses and headstrap e coil calibration block and mounting lug e hex keys and rods e three spare reflector spheres Items may vary according to your site needs Calibration Block The plate has three threaded pins One pin is the point on which you place the hot spot of th
114. r software applications which support multiple docu ments and projects In Brainsight only one project can be open at a time This is reflected in the title of the Data Groups win dow where an unsaved project is named Untitled bproj and an opened or saved project shows its name The project saves the state of all the data essentially a snap shot of all the data at that point You cannot open multiple projects which save as documents in the past doing so com bined them together This is why we have the File gt New Reset Project menu item to clear the current project from Brainsight s memory and enable you to create a new project Resetting creating a New project or opening a project clears the current project as well you will see a Save Project prompt if you choose the File gt Open Project or File gt New Reset Project menus while working on an unsaved project The steps to preparing a study in Brainsight are Il Create a new or open a previously created Brainsight Project 2 Load the images 3 Create 3D reconstructions of the brain and possibly the skin surface of the subject s head Optionally register your images to MNI Talairach space to enable you to use Talairach coordinates as targets 5 Add markers for targets and landmarks 6 Save and quit Brainsight or Save and select New Reset Project to begin preparing a new study For instructions on transfering images from another source to
115. r the Polaris reset sound Second the Polaris Control window opens Most of its settings are configured in the Pref erences window Thus you should not normally have to set or configure ports volumes and tools except the coil tool If the default serial port in the Preferences window has not been set or if the Polaris has not been connected or properly powered up the Polaris does not beep and the Polaris Control window takes several seconds to open Check the connections and the Polaris itself It is important that you always connect the power cable to the Polaris while the power is off not applicable to the Vicra Failure to do so can cause serious damage to the Polaris After the Polaris is connected close and re open the Polaris Control window to reset it After the Polaris is powered up and the Polaris Control win dow is open configure the tools with trackers The controls allow you to load and unload tools activate tracking and set the reference tool controls Figure 7 3 It also allows you to verify the pointer precision and activate the position camera function 46 Brainsight 1 7 Figure 7 3 Polaris Control Tracking ON OF Reference Frame Subject Tracker re Tools Pointer Add Subject Tracker 4 Remove J Tool calibration file P717 txt Tracker ROM file P717 rom Tool visibility A Our of view Reference visibility E Out of view Precision Test N A Position Ca
116. r the draw fill operations then select the Cut line tool and draw an outline of the region to be cleared Figure 8 15 Note that while drawing instead of drawing coloured pixels you are removing pixels from the selected region Once the region has been excised clear the centre by option clicking to invoke the clear region tool the centre of the selection to be cleared to clear fill the region to be erased Repeat steps 6 10 until the structure has been segmented Move the cursor to the bottom of the region you segment ed and on an edge Using the Mesh Seed button drop a mesh seed at that location Click Update mesh The marching cubes operation will march upward and generate the mesh Chapter 8 J 3 14 Ina 3D view pane click on the list selector button and select the newly segmented object The mesh of the seg mented object will appear Curvilinear Tool General Description The Curvilinear Tool allows you to create detailed 3D recon structions of the brain Create a reference surface by drawing guide curves on several slices of a given image plane which act as ribs for the surface The Curvilinear Tool uses the reference surface to automatically create a series of surfaces that are con centric and iso distant from each other at progressively deeper Figure 8 16 cuts It is analogous to peeling the layers of an onion Because the curves are drawn in a single plane they cannot be c
117. rads is Ther al t be enpected shop ree Go bo Previews Step Dane Talairach template overlay 8 When you are finished close the task assistant window or press Done In the Data Groups window the data set will now have one more registration shown in the Information pane Along the bottom of the Volume View window you can now view the co ordinates in Brainsight World or MNI Talairach coordinates as in Figure 7 19 Figure 7 19 ee Brainsight X 90 00 Y 90 00 Z 90 00 World A 1 17 Y 37 79 Z 95 74 in mm Information along bottom of Volume View window If a template file is verified MNI Talairach then after the transformation World becomes Talairach You can load other data sets and if you perform the Talairach reigstration on them you can warp the images to overlay on the main data set the first data set in the Data Groups window Se lect the data set to warp perform the Talairach registration and then click the Warp button in the Data Groups windown You can now select the data set to overlay on the main data set Errors and Troubleshooting From time to time as with all software Brainsight will give you an error code or other unexpected dialog during the per formance of an activity This section presents some of these dialogs in likely chronological order At certain times when using Brainsight the software will look for the Polaris If there is a problem with the connection any
118. required hardware Skip to the next section Install Brainsight on page 8 The hardware required for using Brainsight TMS is the fol lowing e the Macintosh computer e the Polaris or Polaris Vicra optical position sensor e the transcranial magnetic stimulator TMS coil Brainsight TMS optionally comes with a TMS Frame which is not required in order for the system to function It assists in stabilizing the subject and experimental apparatus during the course of the study Its assembly instructions are in Chapter 10 TMS Frame Assembly on page 87 POLARIS The Polaris has two connections refer to Figure 2 1 One is to the power supply and the second is a serial port for the USB serial adapter to the Brainsight computer First connect the pow er supply and then the serial port The camera has two different serial port connections an RS 232 connection and an RS 422 connection Use the RS 232 and ensure that the selector switch between the two ports is set to RS 232 For more information see the Polaris System Guide Connect the Macintosh end of the Polaris serial cable to the serial port on the USB serial adapter Figure 2 2 Connect the USB end of the USB serial adapter to the USB port on the Mac and connect the serial cable to the serial port on the Polaris Re view the documentation of the USB serial adapter to ensure that the correct driver software has been installed and is properly configured After al
119. s optical position sensor contains two infrared cameras emitters and associated electronics It plugs into a power supply and connects to the Brainsight computer by a se rial cable It monitors the space in front of the lenses for trackers see Arrange the Setup on page 13 The spherical reflectors on the trackers require a signal emission in order to reflect their positions to the camera TRACKER A tracker is an object that has reflectors in a pattern recog nizable by the Polaris Each tracker has a unique tool charac terization file ROM file that describes the tracker reflector pattern to the Polaris The orientation of the tracker with respect to the Polaris is important both for accuracy and for consistent tracking See Figure 1 1 for examples of proper and poor tracker orientation Trackers can be attached to various tools for example the coil tracker as shown in Figure 1 2 which 1s attached by a coil ring or tools can have trackers built into them for example the pointer tool as shown in Figure 1 3 The subject tracker is a tracker attached to the subject s head or head holder to monitor the position of the subject s head Chapter l 3 7 Figure 1 3 Bradna T Praeeken a e i Pointer tool TOOLS A tool is an object whose position and orientation is monitored or tracked by the Polaris There are two tools that are common ly used with Brainsight the pointer and the coil tool In t
120. s Mark this Spot 50 you can identify it when asked later Sop inie A Identify the hot spot see the coil manufacturer specifications 3 Click Go to Next Step The dialog in Figure 3 7 appears Figure 3 7 Task Assistant step 2 Attach Tracker to Coil In order for the position ansoar to track tool tracker must be attached to it The tracker comes in three parts A coil handle ning with a hex collar ple Hol Sp on it hex rod which attaches to the hex collar and finally the tracker frame whech also has a hex collar min Attach the ring to the coil handle and then the tracker and her rod a to the coil handle ring Make sure the orientation of the tracker is set to ensure it Faces the position sensor camera during the Epirit Co ape ar Goto Previous Step Go to Next Step J B Attach the tracker to the coil 4 As you have attached the tracker to the coil as shown in Figure 3 5 if this figure represents your coil and tracker type click Go to Next Step The dialog in Figure 3 8 ap pears 18 Brainsight 1 7 E Figure 3 8 i Task Assistant Steps step 3 Enter Pertinent Information Tool Manne The folowing information ig required before cakbratng the coi Enter this information in the F spaces provided Enter lafornaties Coil TR ri ert arne Bat mill h igi E antiy Shi Ejdi lan Et presis fier Auke Bad Tarik FEE Mir Lied a ert od br ba
121. s created in two steps The first step is called segmentation This involves selecting the voxels that define the object we wish to represent as a 3D surface The second step 1s to initiate a process called Marching Cubes which will as the name implies march over the surface of the segmented voxels to create a mesh that can be displayed in the 3D view The starting point of this march 1s defined by a seed point placed on a lower edge of the segmented voxels Control Pane Description The control pane for the Segmentation tool is shown in Fig ure 8 10 The Volume Objects field contains the volume segments you have created The New button will open a new window to allow you to enter the required information to create a new volume object Figure 8 11 The Delete button will delete the currently selected object and the Edit button will open the New dialog box again to allow you to change the name colour or opacity of the object The Opacity slider changes the opacity of the segmented vox els displayed in the 2D view during the segmentation process The Display All check box allows you to view all segments at one time as opposed to the currently selected volumes It will also show all volumes even when another tool e g cursor tool 1s active The Show Volumes button displays a dialog Figure 8 12 that lists the volume calculation in mm of the segmented struc tures After you have clicked on the New button and
122. s directory that contains the ROM characterization files for the tools and the default Talairach template file needed for Talairach mapping 12 Brainsight 1 7 Eg Figure 2 7 Preferences Default NEMA DICOM Philips ANI directory Choose Default MINC and Analyse directory Choose Default tools directory Choose Macintosh HO Tool ROM Files Default Talairach template file MINC format Choose Macintosh HD Users Shared Test lmages average 305 mask mnc Ce ED Default File Paths 8 Inthe Polaris pane Figure 2 8 if your USB serial port is connected and configured select the default port for the Polaris position sensor Figure 2 8 General Default File Paths A Serial port Bluetooth POA Syne Vplemr f Vicra ey Cancel son C Polaris configuration Choose the volume Volume refers to the calibrated vol ume of the Polaris camera Select Extended Pyramid for the standard Polaris and Vicra for the Vicra 9 Click OK to close and save the preferences Chapter 3 Planning a new TMS study Figure 3 1 Illustration of the Polaris s view of the subject The green area indicates the field of view of the Polaris given the setup shown erforming a TMS study can involve coordinating several different activities at the same time Careful preparation can ensure that the experiment is performed accurately and quickly and minimize the chances of an un
123. s in counter clockwise direction and clockwise if you are in normal mode In order to get a consistent depth throughout the surface proper drawing of the guide curves is essential The goal is to have the curve graze the tops of each gyrus Do not try to have the curves dip into the sulci See Figure 8 22 When you have finished drawing the curve for this slice click to another location in the direction perpendicular to the reconstruction plane in one of the other views sagittal or transverse in this example to move the cursor or use your mouse s scroll wheel This changes the slice displayed in the view in which you are drawing the guide curves There are no arbitrary rules as to the spacing of the guide curves you are free to decide how to space them However it helps to have one guide curve in the middle of the brain and one at each extremity in the plane of your choice Then add new guide curves between pairs of existing guide curves to subdivide the sections between them until the interpolated curves agree sufficiently with the actual brain outline Repeat steps 4 and 5 no less than three times To view the results set a view to 3D mode click on the list selector and select the object you just created from the list It will then appear in the 3D view You can manipulate the object in the 3D view as you can with any object and you can also set the peel depth using the slider in the curvilinear tool s control pa
124. s ord M r For HETH Coil or THS Gp Toal ROM File ETT rt a Saelogt Toci hem Fe Ne that a maad eth ihe Eras k er Riel BS Bae Bead Calibration File Name hesrC laktrehO Chere in n re tai bees poe degen from Sher earan boul ace ortho ho Gate Foe initio br byn B col vie nime Bo frp infin FoBDec T Go te Previous Step Go te Next Step 3 Step 3 6 Enter a name for the tool for example coil select the tracker s ROM file and enter the file name for the cali bration file This file is saved to the Tools folder in your Brainsight folder Be sure to choose a name that will make it easier to identify it later during the TMS session For example for a Figure 8 coil use Fig8 Aug10 txt if it was calibrated on August 10 The txt extension is added automatically 7 Click Go to Next Step The dialog in Figure 3 9 appears You should be able to manually hold the coil in position for this process The other two pins on the plate are to help you keep the coil stabilized during this process Their height can be adjusted to accommodate dif ferent coils The correct position is such that the cen tre pin of the calibration block is directly beneath the coils hot spot and the coil held straight so that the centre pin is in line with the field Lining up the calibration block pins with the coils axis helps Brainsight calculate the Inline and Inline 90 views as described in Position the
125. sesencasan 85 Subject Head HOIEL cccccceeceeeeeceeeeeeeaeeeeeees 85 Forehead Rest and Coil Holder Articulated Arm 85 Chapter 10 TMS Frame Assembly 87 Assembling The A Frame Second Generation Frame 87 Using The Frame For Subjects Sitting Up 90 REPOSITIONING THE TMS FRAME ceseceseeseveveceeeeeavavaeees 91 Setting Up the TMS Chair Coil Holder Third Genera tion System ee 92 NS se sa EE 92 OPERATING THE CHAIR suavvnvvnnvnvnnvvnrnnnnnnvnrnnevnnvnernevnennne 96 Index 97 Feedback 101 Legal Terms and Conditions End User Software License Agreement Please read this Software License Agreement carefully before using the Software By using the Software you are agreeing to be bound by the terms of this license If you do not agree to the terms of this license promptly return the Software to Rogue Research Inc ROGUE RESEARCH INC AND ITS SUPPLIERS DO NOT AND CANNOT WARRANT THE PERFORMANCE OR RE SULTS YOU MAY OBTAIN BY USING THE SOFTWARE OR DOCUMENTATION ROGUE RESEARCH AND ITS SUPPLI ERS MAKE NO WARRANTIES EXPRESSED OR IMPLIED AS TO NON INFRINGEMENT OF THIRD PARTY RIGHTS MERCHANTABILITY OR FITNESS FOR ANY PARTICU LAR PURPOSE ANY LIABILITY DUE TO FAILURE OF BRAINSIGHT WITHIN THE ONE 1 YEAR WARRANTY PERIOD SHALL BE LIMITED TO REPLACEMENT OF THE SOFTWARE AND OR THE REPAIR OF BRAINSIGHT EQUIP MENT IN NO EVENT WILL ROGUE RESEARCH OR ITS SUPPLIERS BE LIABLE TO YOU FOR ANY CO
126. set screw while ensuring that the screw itself comes in contact with one of the faces of the hex rod rather than an edge between two faces Loosen the set screw on the tracker collar and place the tracker on the hex rod now attached to the coil collar Rotate the tracker around the rod so that it faces the Polaris when you are using it for stimulation on the subject using the principle as described for the subject tracker see Figure 3 1 and Figure 1 1 for proper tracker orientation Tighten the set screw while ensuring that the screw itself comes in contact with one of the faces of the hex rod rather than an edge between two faces Calibrate the TMS Coil Coil calibration using a calibration block is quite simple The menu item to perform a coil calibration is Window gt Calibrate Coil FOLLOWING THE CALIBRATE COIL TASK ASSISTANT Prior to beginning this procedure plug in and turn on in the case of the standard Polaris the Polaris optical position sensor in order to give it time to warm up l In Brainsight select Window gt Calibrate Coil Fol low the steps in the Task Assistant window as shown in Figure 3 6 Identify the coil hotspot Chapter 3 17 7 0 Task Assistant Step 1 Identify Cod Hot Spot In onder to track cod spot must be identified on the coil that comesponds to the coil s hot spot In Bramsight this wil be the spot used Lo show the locaton of the coil on the image
127. station copy the images Chapter 4 23 ks from the archive to a mass storage device or disk such as an ex ternal hard drive or CD ROM and mount that disk on the Brain sight computer After it mounts the images can simply be copied from the storage device to a folder on the Brainsight computer About Storage Media There are many other types of disk media and disk formats It is important to note that it is not just the actual disk media that counts but the disk format as well Before copying files from a CD ROM the format of the CD must be established The Brain sight computer likely has a CD ROM drive installed This drive can read many common CD formats Make sure that it is sup ported on the Macintosh workstation If a disk containing data fails to mount or if an operating system error appears talk to your system administrator or contact Rogue Research COPYING FILES TO THE BRAINSIGHT COMPUTER The steps required to copy images to and from a CD ROM or other external disk are the following 1 Mount the disk by inserting it into the appropriate work station drive or attach it by cable to one of the ports on the back of the archive workstation 2 Copy the image files to the disk You should be familiar with the file naming strategy and folder tree on the disc If you are not contact the person who created the direc tory Eject the disk On the Brainsight computer create a new folder for the image files 5
128. supports a new TTL and switch based trigger method for the rapid fire annotations and trajecto ries The LabJack Chapter 2 Installing Brainsight Figure 2 1 To USB port On Macintosh U amp BCable U amp B gt Serial Adapter Serial Cable DEG h J f B TET r Polaris Camera rear view Polaris Power Supply To AC Power via Surge Suppressor Connection hook ups between Macintosh compu ter and Polaris It is important to always connect the power cable to the Polaris while the power is off Failure to do so can cause serious damage to the Polaris Figure 2 2 USB Serial adapter his chapter is for primarily for new users installing Brain sight TMS and its associated hardware for the first time for assembling the TMS Frame and a description of hardware components and their care refer to Chapter 9 and Chapter 10 It also applies to users who have recently upgraded from Mac OS 9 to the required Mac OS X operating system Upgrading from a previous version of Brainsight has no special steps or considerations it is like a new installation as described in this chapter For meanings of terms specific to using the Macintosh for example shift click access Mac Help by the Help menu in the Finder We assume you are familiar with Mac OS X Install and Connect the Hardware If you already use a previous version of Brainsight and you are upgrading you already have all the
129. t as shown above Chapter 8 1 TT Figure 8 26 Target used for positioning Trajectory uted for positioning Desired coetex to stimulate Actual trajectory Illustration of the increased robustness of cortex based targets Left image shows a correctly placed coil over a target and trajectory defined at the cor tex Right image shows the coil placed over the cortex based target with a similar error in trajectory as described in Figure 8 25 In this case since the coil is still pointing to the target e g using the trajectory targetting bull s eye the desired brain tissue will still get stimulated albeit from a slightly different angle Step 2 Configure a 3D view to see the surface and a rep resentation of the cursor e g cursor sphere or trajectory stick Configure 2 of the 2D views to display the inline and inline 90 views Figure 8 27 OB ess teas BQ maa BQ v i J Preferred layout for placing a grid MM aaeo Step 3 Use the 3D cursor tool to select the centre spot where you wish to place a grid Note that when you use the 3D cursor tool to click on a sur face the orientation of the display as seen by the inline and inline 90 and 3D view will automatically be set to the normal to the surface at the click point 18 Brainsight 1 7 ESE n Figure 8 28 E Grid Cesira Label Grid 1 Angular Input Row 3 Columns 3 mel skrin Row Spacing 500 Column Spacing 5 00 Cote OY Hiigiht
130. te at http www rogue research com Brainsight First Run The first time you run Brainsight you need to review and update the preferences s with the previous version and with other Macintosh applications launch Brainsight by double clicking on the Brainsight brain icon You can also drag the Brainsight icon to the Dock so that you can launch it from there in the future SETTING PREFERENCES 1 Have your USB serial adapter or Vicra dongle plugged in to your computer and the necessary drivers installed 2 Connect the Polaris to the power supply if there is a power switch as is the case on the Polaris and not the case for the Vicra turn it on 3 Launch Brainsight Enter the serial number at the prompt Make sure you also type in the dashes and then press OK If the OK button remains disabled then you have mis typed the serial number or the number you have is invalid Contact Rogue Research to get a new number if the number you have does not work 5 Yoy may be prompted for your Administrator password so Brainsight can correctly set the file permissions of several files including the preferences file 6 Select Brainsight gt Preferences The window in Fig ure 2 6 appears Chapter 2 1 Figure 2 6 Preferences Ge meral Default File Paths Polaris Surface render view background colour Volume cursor colour EE Normal annotation colour _ Highlighted annotation colour 2D annotat
131. te at an early stage of a study Brainsight prompts you for a file name Fill in a name and press Enter When naming the project the software appends bproj as the extension This helps you distinguish the Brain sight project file from other types of files After the first save subsequent saves File gt Save or Com mand S automatically save to the project file When creating a new project Command N or File gt New Reset Project opening another project File gt Open Project or Command O or quitting the application Brainsight prompts you to save the project if you ve made changes since your last save This eliminates the possibility of accidentally quitting the application without saving your work This also gives you the 30 Brainsight 1 7 LCI Figure 5 7 e f Curve drawing grazing the top of the sulci depth generation during reconstruction mechanism to revert a project to its last save point by choosing Don t Save Prepare the Project for the Study These are the following tasks in this section l1 Perform a 3D reconstruction of the brain 2 Perform a skin segmentation of the subject s head 3 Optionally register the anatomical images to MNI Ta lairach space 4 Select landmarks and targets for the subject image regis tration and for the area of study Perform a 3D Reconstruction Curvilinear reconstruction helps you view the brain and plan the experiment It is not alw
132. ter as a reference to the user interface of Brain sight TMS Although you may already be familiar with Brainsight you will find a review of this material helpful For meanings of terms specific to using the Macintosh for ex ample shift click access Mac Help from the Help menu in the Finder We assume you are familiar with Mac OS X Remember that the Command key has a symbol on it Menus Brainsight About Brainsight TMS displays the About box which con tains the version number of the software a warning or acknowl edgement of its intended use and the copyright information Preferences allows you to configure the general prefer ences for how data is displayed where specific files are located and how your position sensor operates File New Reset Project clears the current project from Brain sight s memory essentially creating a new project If the current project has any data in it this command also prompts you to save it before it 1s cleared Open Project opens a pre existing Brainsight project Use this option for subjects whose data you have prepared for a study and to open completed studies Import Images is the first step to create a new project by importing a subject s MRI scan import anatomical images first You can also import data to overlay on image data in an existing project See Figure 7 1 for the Import Images options and key board shortcuts Close closes the frontmost Volume Vi
133. ter to various positions on the subject s head and cheenve where the point les on the images if the Brainsight cursor agrert sulhcently with the pointer this rask ic complata rrharvdsn do on ol the following 1 ek che G t Pred Step button f reat the Sanh Point steg to try bo imanie the registration A P Le the mariner tool to correct or add anatomical landmarks Press the Go bo Previous Mep button to repast the registration Aa fina inte Go fo Previous Sep Doane Step 4 The Task Assistant automatically sets Brainsight to use the pointer as the cursor input Verify the registration by placing the pointer at various locations around the head and check that the cursor on the screen agrees with the pointer location If the registration is acceptable click the Done button to close the Task Assistant window to complete the regis tration process If it is not click Go to Previous Step to repeat the registration Position the Coil l If you have not already done so set one of the image views to 3D to display the 3D curvilinear surface Click on the 3D Object selection button in the 3D view and then select the box next to the name of the surface family see Creating a Curvilinear Reconstruction on page 30 Scroll to Axes Probes and select either pointer stick pointer lines or pointer sphere and Figure 8 Coil if so desired to add a representation of the coil location Clic
134. the Brainsight computer see Chapter 4 Reload a Project To reload any project find the project file and double click it Note Do not use this method if you have multiple versions of Brainsight on your computer e drag it to the Brainsight TMS application icon in the Dock e launch Brainsight and select File gt Open Project Com mand O Select the project as shown in Figure 5 1 Brainsight 1 7 E Figure 5 1 akaf Open a i 3 Dotuments H4 q search P nerwork staller Log AM Flan review pdf E ns j apwall pg a Data F broc utter pr nN e 4 3 content lopment J Heia s cancer iil L eBooks i E FE Desktop F27 hpraj R jane r a F 8 bproj a 2 feb Lbproj olications 1 ie Hame March se App FER 2 bpraj 23 bpre r po Bii oi Os DOT Ti r gt Documents ine 17 5 MB i 1 a Mi bora Kind Brainsight ia Movies ml bproj r 17 Project March 22 bpro 7 Created 22 03 06 Music H EREINA li 257 PM New Folder Cancel F Open Open Project dialog with Brainsight Project icon To reload a recently used project you can use the Apple gt Recent Items menu if it is displayed in the Documents sub menu If the project file referenced any images Brainsight loads them If it cannot find the images if they were moved or the directory structure changed Brainsight prompts you to select them When you load a project any guide curves from cur
135. the previous movie to start a new movie using the same name In order to stop recording and write the movie to file press the rectangular Stop button Close the window after stop ping the record process PRINT VIEW This function takes a snapshot of the current view and sends it to the printer There are no options to control the print size or to include annotations in the printed image 2D Mode The 2D mode displays individual slices of the MRI scan in different orientations The tools available to the 2D mode are described here Note that the tools common to the 2D and 3D modes have been described earlier in this section 2D IMAGE VIEW The 2D view mode controls allow you to select one of the available image planes to view and allows you to export the image in the view to an external file QuickTime movie or to a printer See Figure 7 8 Figure 7 8 BQ Transverse 2D view tools VIEW SELECTION Select the viewing plane by clicking on the View pop up menu The standard views are grouped into three categories Il multi planar reformatting MPR which includes the familiar sagittal coronal and transverse planes 2 oblique views which include in line in line 90 and per pendicular F igure 7 10 Object Rotation Chapter EE 3 targeting view for markers and trajectories which ap pears as a bull s eye It displays the shortest distance from the coil s trajec
136. the regions of the structure you want to segment Click either Prev Slice or Next Slice to move to the adjacent slice and bring the seeds along The seeds from the previous slice will propagate to the new current slice and re apply Verify that the structure to be segmented has been delineated If a region was left out and falls within the threshold highlighted then drop another seed in the region If one of the seeds fell outside the region of interest and is selecting unwanted regions select the Clear Slice tool and click on the image to clear all fills and remove all seeds Adjust the threshold if required and drop new seeds in the highlighted regions to select the region of interest If part of the region of interest falls outside of the thresh old you can draw it manually to select it Select the Draw Line tool and draw a closed outline around the region of interest see figure 8 14 Select the Fill tool and click inside the region of interest The fill operation will start at the click point and flood until it reaches the outline drawn in the previous step or any other pixels that were selected Alternatively short cut instead of selecting the fill tool remain in the draw line tool and option click to perform a fill operation This allows you to rapidly draw and fill several regions without switching tools If you need to clear a region that was selected either with the seed threshold fill o
137. the tracker on either side of the subject s head There is also a hole in the lenses allowing access to the nasion the bridge of the nose during the subject image registration In addition to selecting the fixation method place the tracker in the hex rod collar in such a way that the tracker faces the camera during the experiment see Figure 1 1 Configure the Coil for Use Attach the Coil Tracker As with the subject Brainsight monitors the position and ori entation of the coil by attaching a tracker to it Instead of a head strap or glasses the coil tracker is fixed to the coil using a hex rod and a coil specific adapter usually a ring The coil ring is a round ring cut in half and 1s attached to the TMS coil handle see Figure 3 5 The ring includes a fixation collar that fits a hex rod onto which the TMS coil tracker is attached Different sized coil rings can be attached for TMS coils with different shaped handles Other adapters are available for certain coils 1n cases where a ring 1s not suitable ATTACHING THE COIL TRACKER Il Attach the ring to the coil handle as shown in Figure 3 5 Use the included hex tool to tighten the two screws until the ring 1s secure 16 Brainsight 1 7 Er Figure 3 5 The coil ring comes in two halves that are placed around the handle of the TMS coil 2 After the ring is attached loosen the set screw on the hex collar and insert the hex rod into the collar Tighten the
138. the view automatically adapt depending on the mode You can change from 2D to 3D mode by selecting either the 2D or 3D view mode buttons on each image view pane See Figure 7 6 The following tools are available in both view modes e export view to file e export view to QuickTime movie print view EXPORT VIEW TO FILE Clicking on the Export button activates a dialog requesting the file format for the new image file Select the format then enter a name for the file and press Save 50 Brainsight 1 7 e EXPORT VIEW TO QUICKTIME MOVIE ess Figure 7 7 5 QuickTime Record Filename Untithled muv Frame number 0 E QuickTime Movie Record Controls Transverse This function allows you to link a view to a QuickTime movie to save a dynamic view of your images Every time the view is updated in any way a new frame is added to the movie Clicking the Export to QuickTime button prompts you to enter a name for the new QuickTime movie file Press Save A recording control window appears Figure 7 7 This window controls the movie recording process Pressing the red record button starts the process Every time the view is updated a new frame is appended to the movie If you want to pause the recording press the Pause button This suspends the recording process but keeps track of where you are in the movie Press Pause again to resume recording If you press record again it erases
139. tical bar and secure it by tightening all the T nuts Add the forehead rest mounting plate to the top of the vertical bar using the 4 bolts that are supplied with the mounting plate Figure 10 19 Add the 2 sliding accessory blocks to the coil arm rails by removing the end caps sliding the blocks onto the rails and replacing the end caps Add the chair to the stand Have an assistant hold the retaining pin of the chair mounting block open by pull ing the cable attached to the pin at the base of the block While holding the pin open lower the chair so that the round metal flange at the base of the chair fits into the brass receptacle of the base Twist the chair back and forth until the flange is completely into the base Release the pin The pin is designed to fix the chair at the 0 and 180 orientations Once locked into place the chair will not ro tate unless the pin is released by pulling on the wire under the chair Chapter 10 95 Es 11 Insert the head rest into the chair 12 Add the forehead rest and coil holder arms by inserting the ends into the receptacles of the forehead rest mount ing plate and one of the sliding accessory blocks respec tively Figure 10 20 Note that there is a flat spot on the cylindrical ends of the arms Align the flat spot with the Figure 10 20 Top of stand with head rest and the arms in place Figure 10 21 retaining set screw on the mount to prevent the arm from twisting in the
140. to position the camera so that the tool is well within the volume The box represents the shape of the field of view of the camera and the green dot represents the location of the tool currently selected in the tools list The small dot is green when inside the calibrated volume The dot disappears when the pointer exits the volume Precision Test This function tests the precision of a pointer tool when you suspect the spheres have been damaged or the pointer shaft has been bent The button initiates and ends the precision test The precision test 1s done by placing the tip of the pointer into a divot hole in the old or new calibration block or any fixed location and clicking on the Precision Test button Brainsight stores the current pointer location and the Polaris takes samples while you rotate the pointer The display shows the maximum position error encountered while moving the pointer When the test is complete click the Precision Test button again Contact Rogue Research to find out if a precision test is nec essary and to obtain the expected results for the precision test according to your pointer tool 18 Brainsight 1 7 mesen Figure 7 5 GMP roch mrl corrected minc 1 Layout Tool B mi 4 ss LE Selector 01 Bar Hofu MO armere siGla h D alala M Maso Pow 1 Sjal I ER Mate E Tip Of van Tool Control Dinara To Marie Lr arrir arp Pane Dinuga s n TT Mather haters F
141. to the collar 3 Turn the hex rod until a flat face of the rod faces the set screw in the collar 4 Using the hex hey tighten the set screw while ensuring that the screw itself comes in contact with one of the faces of the hex rod rather than an edge between two faces The head strap is the most common method of attaching a tracker to the subject head It is comfortable and securely holds the tracker on the head The elastic band has Velcro on the ends allowing you to tailor the length to fit different head sizes Chapter 3 15 I The collar allows you to insert the hex rod in one of two holes either vertically or horizontally to ensure that you can find an orientation that best presents the tracker to the camera See Figure 3 4 for hex rod attachment and see Figure 3 1 and Fig ure l 1 for proper tracker orientation Figure 3 4 Examples of where the hex rods go into collars to attach a tracker to the subject The glasses have a collar at both ends of the frame The head strap has a single collar however the collar has two holes one horizontal and one vertical to allow more flexibility in positioning the tracker In cases where the elastic strap interferes with other objects on the head for example if the subject is wearing EEG elec trodes a pair of glasses equipped with fixation collars for the subject tracker can be used The glasses have fixation collars at either end of the frames allowing you to put
142. tomat1 cally created whenever a signal is received from the X keys Switch which happens when the TMS coil is fired 8 When the experiment is complete deselect the Active checkbox to stop monitoring the stimulator LabJack Interface More recently a new interface was adopted based on a La bJack analog to digital acquisition system The box has a USB connector and two BMC connectors Connect the USB to your Macintosh do not use a USB connector on the keyboard One BNC connector is designed to accept TTL pulses e g from the stimulator and requires a TTL pulse width of at least 200usec and can accept both low high and high low signal triggering The second BNC can be connected to any switch for manual triggering Maintenance Polaris Optical Position Sensor Refer to the Polaris System Guide for maintenance instructions Tracker Spheres Dust can be removed from a reflective sphere using com pressed air or by lightly brushing it with a photographic lens brush Trackers and Tools Clean with a lint free cloth If required dampen the cloth with water or water and mild soap Do not use water or soap on the spheres Head Strap Clean the strap and foam pad with a cloth dampened with wa ter and mild soap Do not use any detergents that can cause skin irritations when wearing the strap Tracker Glasses The glasses frame can be cleaned with a cloth dampened with water and mild soap The lenses can be cleaned
143. tory to the target The oblique views are arbitrarily oriented viewing planes that are normally used when the display is being driven by a tracked tool such as the pointer or coil The display can also be control led off line by opening the manual trajectory interface Win dow gt Manual Input and selecting it to drive the display 3D Mode The tools available to the 3D mode are described here 3D IMAGE VIEW The 3D view mode controls allow you to take any of the 2D planes and display them in a 3D context This view can give you a better understanding of the three dimensional relationships of the various structures Because interaction with the 3D view is different from the 2D view it uses a different series of tools See Figure 7 9 Figure 7 9 og A 3D view tools Fl aea CAMERA ZOOM This tool allows you to change the magnification of the ob jects in the 3D view To use it select the tool click the mouse in the view and while holding the mouse button down drag the mouse up to zoom in and down to zoom out The rate at which you approach or move away from the objects is proportional to the amount of movement of the mouse that is a large mouse movement makes the zoom fast TRANSLATE OBJECTS This tool allows you to move your point of view up down left and right Select the tool and click the mouse in the view While holding the mouse down move it in any direction you wish to move the objects ROT
144. uctures 66 annotations distance between 63 distance to current 62 export button 64 list of markers 63 Rapid Fire 64 registration landmarks 33 annotation targeting 38 See also bull s eye view Annotation tool 63 64 control pane 63 Assisted Registration 35 Axes Probes 38 B Brightness Contrast threshold threshold 49 bull s eye view See targeting view using 38 C calibration file 46 camera location 13 20 See also position sensor Polaris 2 zoom 51 coil attaching the tracker 15 holder 85 91 location 38 Pointer Mode 39 61 tool See also tools coil tracker 2 82 Coil Calibration 16 block 81 vl 0 44 Command key 1 43 connecting cables 7 Rapid Fire 41 X keys Switch 41 control pane 61 80 using Rapid Fire 41 coordinates 64 coronal See image view selection Cursor tool control pane 61 curvilinear reconstruction 30 surface family 72 surface family preferences 74 Curvilinear tool control pane 71 75 using 30 34 38 D description Brainsight 2 hardware terms 2 81 86 ROM file 3 software 3 43 60 dialogue See window distance between image objects 63 dropping amarker 63 E EEG 15 83 electroencephalography See EEG environment See operating system export annotations 64 image 41 49 QuickTime movie 41 50 F file path default preferences 43 file type ACR NEMA 27 Locator 44 MINC 21 forehead rest 85 Frameless Stereotaxy 1 98 Index EE frame levers 91 FTP 22 23 f
145. ull s eye view to help manipulate the coil location with respect to the target Using a Trajectory to place the coil There are many instances where you might want to replicate a position and orientation of the coil for targeting For example you may have created a grid of trajectories to perform a mapping exercise or you wish to replicate a stimulation recorded during a previous session In either case the trajectory targeting bull s eye view will be helpful The bull s eye view for markers displays a simple crosshair representing the center of the coil and a dot representing the target The bull s eye view for trajectory builds on that by adding representations of the angle of the coil as well as the twist relative to the trajectory Figure 6 7 illustrates how the bull s eye relates the desired target position and approach trajectory to the coil s position and orientation Think of the Bull s eye as a plane on the face of the coil The trajectory target projects towards the coil and the bull s eye A green circle is displayed 4 Brainsight 1 7 ae Figure 6 7 Planned Planned Trajectory Trajectory Bull s Eye at Coil Face TMS Cail Projection Targel where the trajectory hits the bull s eye plane think of it as the scalp entry point The target itself is projected to the plane in Figure 6 8 the same manner as with the marker bull s eye that is taking the shortest path fro
146. unctional image overlay 28 G guide curve indicator 72 H hardware 81 86 cleaning and maintenance 85 86 connecting 7 description 81 85 installing 7 12 header file See hdr head strap 85 See also subject tracker I image 2D 50 3D 51 controls 49 print 49 50 view pane See pane Image View view selection 50 images folder organization 21 opening 28 image types anatomical 28 fMRI 28 functional 28 overlay 28 PET 28 imaging convention 73 setting 11 importing images anatomical 28 File menu 27 functional 28 inline and inline 90 19 38 installing hardware 7 L Landmarks 33 launching Brainsight 10 layout 49 selector 49 location camera 13 15 See also position sensor Locator 44 M Macintosh 1 application preferences 9 file copy 22 23 multiple users 9 Mac OSX 7 Dock 10 Magnetic Resonance Images ing See MRI Manual Pointer 51 MINC 21 MPR 50 3D object view 52 MRI 1 file archive 21 folder organization 21 laboratory scanner 21 Slices 50 multi planar reformatting See MPR N Neurology convention setting 11 O object translation 51 oblique views See 2D view selection offset 30 31 ROM file information 46 open images 28 operating system error 23 UNIX 21 22 orientation tracker 2 orientation selection 53 overlay functional images 28 P page setup 43 pane Image View 49 tool control 61 peel curvilinear surface 71 perpendicular See image view selection pointer 3 81
147. value must be pro grammed as a character at both the X keys Switch and the Rapid Fire trigger When Brainsight receives this character it triggers the Rapid Fire feature of either the Trajectory or Marker tool to automatically drop a marker Rapid Fire behaves as if you had typed that key on the keyboard The X keys switch is manufactured by P I Engineering Their website is http www xkeys com CONNECTING THE X KEYS SWITCH Il Ensure that the trigger is set to output a signal that goes low see Figure 9 5 during stimulation refer to the stim Figure 9 5 ulator documentation 2 Connect the TMS trigger or manual hand switch pick le output to a switch input of the X keys Switch using 1 ie the appropriate cable and adapter 0 3 Connect the USB cable from the X keys Switch X Keys No Yes USB to the Brainsight computer 4 Note the character associated with that particular switch Ensure that the TMS trigger output is configured port to go from logical I to logical 0 when the coil is fired 5 When in the course of the study you are ready to record points click on the Rapid Fire button in the Marker or Trajectory tool 6 Select Keyboard In the Key field enter the keyboard character associated with the X keys Switch port Figure 9 5 LabJack UsS LV LabJack interface with BNC connectors for TTL and switch triggering Chapter 9 8 7 Enable the Active checkbox new marker is au
148. ves and other mountable storage media e Network transfer File Transfer Protocol Secure Copy and file sharing e DICOM server application transfer Regardless of the method of transferring images from the MRI laboratory s scanner workstation referred to as an archive there are some initial concepts and actions you need to address at your Brainsight computer The issues are the following e folder organization for MRI files used by Brainsight server addresses user names and passwords at the ar chive computer and for local File Transfer Protocol FTP software Prepare the Brainsight Images Folder It is important to properly organize files on a computer hard disk for quick and easy access and minimize software file errors Managing image files can be deceptively complex particularly if more than one scan is analysed A simple folder organizational strategy is shown in Figure 4 1 create a root folder called Subject Data Inside the folder Subject Data place individual folders for each subject You can use the subject s name or some identifying piece of information likely not to be duplicated Both forms of identification can be used as in Figure 4 1 If there is only one scan for that subject you can place that image file in their general folder We recommend that you create sequential scan folders within the subject s general ized folder to accommodate this possibility Direct DICOM Transfer There are public
149. vilinear reconstructions are reloaded and the 3D reconstruction occurs automatically Brainsight 1 5 or Earlier Projects If your project was created using v1 5 Brainsight prompts you to save it under a new name It also appends bproj as the file extension for 1 7 projects See Figures 5 2 and 5 3 Figure 5 2 This project was saved In Bralnsight 1 5 format and must now be resaved in Brainsight 1 7 format The original Brainsight 1 5 project file will not be altered and subsequent changes you make affect only the Brainsight 1 7 project file Brainsight 1 5 cannot open Brainsight 1 7 projects Project file conversion dialog Analyze Format Issues Most implementations of this format omit the orientation information The orientation field is present in the header and when left blank reads to the computer as 0 Unfortunately 0 is defined in the Analyze format as transverse not undefined Therefore when using this format you must ensure that the orientation field is properly set or the images must be restricted to transverse Chapter 2 TEE Figure 5 3 NE Save Choose a name and location to resave your project in Brainsight 1 7 format Hi Desktap H Q search 7033 B ron iso 88 2 6700339 ron 27 pnrg u Applications HEKI Save As Untitled bprod Bia 2 ILNSK Network mj Macintosh HD Applications BillElectrodes 0506 Y Desktop Brainsight EEG A
150. with a lint free cloth either dampened with water and mild soap or a lens cleaning solution Subject Head Holder Clean with a lint free cloth If required dampen the cloth with water and mild soap Forehead Rest and Coil Holder Articulated Arm Clean with a lint free cloth If required dampen the cloth with water and mild soap Do not add lubricant to the ball joint Arm 86 Brainsight 1 7 SSS tees slippage can result when bearing weight Forehead rest pads may be cleaned by soaking them in water and mild detergent Replacements are available for when they become worn Contact Rogue Research or your local distributor for details Chapter 10 TMS Frame Assembly he TMS Frame or subject head and coil holder consists of several parts e Main frame assembly which consists of the legs and adjustable vertical bar e Accessory mounting frame which serves to hold the head holder and coil holder parts There are two frames used with Brainsight legacy C frames consult your v1 5 documentation and the A frame as docu mented here Assembling The A Frame Second Generation Frame 1 Open the box and lay out parts as in Figure 10 1 Figure 10 1 Unpacked frame ready for assembly 88 Brainsight 1 7 SaaS Sag 2 Assemble left and right legs a Loosen T nuts on L brackets just enough so that the T nut fits into the extrusion slot in legs without falling off b P

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