Home

MCW ¤¥¦¨ User Manual Medical College of Wisconsin

1. d g Commissure are n a nnn nnn n enn n eee e eee See eee ee nents ee Inferior lt Ea E Edge of PC ll Supi Airanior Posterior Cerebral Edge of AC Commissure Margin of AC Aqueduct Ny Cartoon of central brain showing key anatomical locations To select the landmarks you must first choose Allow edits so that AFNI will let you change the markers After that you choose the five landmarks AC superior edge The highest point on the anterior commissure in the mid sagittal plane AC posterior margin The rearmost point on the anterior commissure in the mid sagittal plane PC inferior edge The lowest point on the posterior commissure in the mid sagittal plane First mid sag pt Two points are required in the longitudinal fissure they are used to define the new z axis Two points are required to make sure that the new vertical plane is defined adequately the mismatch between the AC PC line and these two points must be less than 2 Another mid sag pt Should be at least 20 mm away from the first one AC superior edge E Allow edits anterior point w Allow edits AC posterior margin posterior poin p 8 Pcolor white t j j Pcolor white PC inferior edge superior point i Scolor limegreen m Scolor limegreen M7 First mid sag pt inferior point i i Si F Another mid sag pt left point a right point ZR E z Set Clear amp i Set Clear E Big Talairach Box Or
2. i m See Markers j x cad F rl fa a i Gap Fr Define Function f 79 EFF A iN r See Function Axial Image IG Py me Def ine Datamode EERE Imagel Coronal Image fy Switch Session Switch Anatomy New Views Switch Function BHelp SSS short Disp Save one Mont AFNI controller and image viewing windows 4 2 Program Control At the lower left of the control panel are four buttons which control various global pro gram functions This button will open up a new AFNI controller window In this way it is possible to open up image viewers on more than one dataset or session at a time A maximum of 5 controller windows can be open at once The first controller window and its children are marked with A in their titlebars the second is marked with B and so forth This button will open and close the control panels to the right of the first column of the controller window the first such control panel starts with Original View in the figure above This function allows you to save some screen space without iconifying the controller window BHelp This button allows you to popup a help window for most controls within AFNI Pressing BHelp will cause the mouse cursor to change to a small hand shape Pressing MCW AFNI 2 00 11 Dec 30 1996 kK oa Left is Right mouse Button 1 while the hand is over an AFNI control will popup a help window for that control Clickin
3. These are similar in concept to the fith images but the threshold data now has the statistical parameters e g degrees of freedom attached that allow calculation of the significance p level With such a dataset AFNI will interactively display the p value associated with the chosen threshold At present only AFNI and 3dfim generated fico 3dttest generated fitt and 3dANOVA generated fift datasets have the statistical parameters automatically attached Using the new to3d it is possible to create your own datasets of these types if you provide the needed auxiliary statistical parameters Demise of Dataset Name and Short Label These values are no longer used in to3d or AFNI The filename of a dataset is now used for display in the AFNI window titlebars and selection choosers The original purpose of the name and short label values was to assign descriptions to a dataset that did not depend on the filename This is needed when one dataset refers to another which happens during the warp on demand procedure If you renamed a dataset and if filenames were used as the internal method of keeping track of such references AFNI would get confused To solve this problem I have instead put inside each dataset s HEAD file an internally generated identifier code This is designed to be unique and independent of filenames When you run an AFNI program on an old MCW AFNI 2 00 4 Dec 30 1996 dataset you will see a message that i
4. and ort waveforms should be plotted or just the first columns Compute FIM This will start the correlation calculations At the least an ideal waveform must be specified before this button will work You may also wish to set the Ignore value and the ort waveform prior to these computations The calculations use the recursive method of Cox et al 4 While they are proceeding a progress meter will display over the titlebar of the AFNI controller window When the results are finished the new fico dataset will become the current functional dataset and can be examined immediately in the image viewers If the input 3D time dataset were named elvis orig then the fico dataset will be named elvis orig where will be one of 1 2 3 If desired the Dataset Rename plug_rename c plugin can be used to change the prefix to something more convenient 4 5 Viewing Controls The second column of the AFNI control window contains many controls that affect how the datasets are viewed transformed and output 4 5 1 View Modes At the top of this second column are the view mode controls These let you switch between the available views Original AC PC aligned or Talairach If a particular view is not available for the currently active anatomical dataset then the corresponding button will be inactive grayed out When you switch view modes you will see that the windows change size That is because in the acpc and tlrc views the
5. it is possible to view several datasets at once in several sets of viewing and graphing windows Normally the view points of the separate controllers are independent that is clicking in the sagittal window of controller A will change the viewpoint of A s coronal and axial windows but will have no effect on B s image and graph windows Under some circumstances you may wish to lock some controllers together so that their viewer windows move in unison This can be done with the menu There is only one lock in AF NI This menu determines which controller windows participate in the lock If the spatial viewpoint is changed in any window that is affected by the lock then AFNI will attempt to jump all other locked windows to the corresponding viewpoint In addition the menu has a button to detach all controllers from the lock and an button which can be used to make all viewer windows affected jump to the locked position Enforce is only needed just after choosing which controllers to be locked together A couple of applications for the lock e Scrolling through several anatomies in Talairach coordinates simultaneously viewing the similarities and differences e Viewing a dataset in Original and Talairach coordinates simultaneously e Comparing several different functional datasets overlaid on the same anatomy AFNI can have trouble when the lock is used between controllers in different coordinate sys tems The lock subrouti
6. The two built in functions are and OSfilt3 which are order statistics smoothing filters using a 3 wide neighborhood In addition the plug_lsqfit plugin defines two more functions which can be used to do linear least squares fits of various functions to dataset time series Normally if a transformation is applied the graph of the trans formed data replaces the graph of the original data If this item is selected then both graphs will be displayed This was added to be able to see the least squares fits from plug_lsqfit plotted over the input data This closes the graphing window the keystroke q has the same effect 4 4 3 menu This menu is used to control the computation of functional datasets of the fico type from 3D time datasets Some of the functions of this menu are duplicated on the Function control panel menu Theory of FIM If x is a data time series and r is a known reference or ideal vector corresponding to the expected activation time course then the statistical model for x is In Arn tat bn m n 0 1 m N 0 0 iid where is the unknown amplitude of the activation a is the unknown mean signal level b is the unknown linear drift in time and g is the unknown noise variance The correlation MCW AFNI 2 00 22 Dec 30 1996 method 2 4 computes the sample correlation coefficient between xz and rn and uses that to determine the significance of the hypothesis that a 0 Time S
7. and 64 bit complex numbers complex datum The purpose of the byte datum is to allow for compact storage of datasets where the 0 255 range has sufficient precision The purpose of the float datum is to allow for more natural storage of statistical quantities without the need for rescaling to the limited range of values allowed with shorts But see item 2 below The purpose of the complex datum is to eventually allow for unprocessed reconstructed images to be directly imported into AF NI Scale Factors Each 3D sub brick in a dataset can now have a floating point scale factor attached to it The purpose of this is to allow data to be stored in the more compact byte or short formats but always to be automatically scaled to the correct units when accessed by an MCW AFNI program For example correlation coefficients can still be stored as shorts 10000 10000 but will be scaled by 0 0001 to their true range 1 0 1 0 before being displayed or processed The new interactive FIM utility in AFNI does this see item 6 below The new to3d can take as input floating point volumes and scale them to produce short or byte datasets with the appropriate scale factor s attached Auxiliary Statistical Data There are three new types of datasets the fico fitt and fift functions fico means functional intensity with correlation fitt means functional intensity with t test fift means functional intensity with F test
8. be warp on demand until and unless you write out the BRIK files using one of the Write buttons described later The transformation from orig to acpc in the anat dataset stored in the HEAD file will be applied to the other datasets in the torig view These follower datasets are what makes AFNI work and easy to use When the anat transformation from acpc to tlrc is defined when the X is placed at the top of the third column then all the other datasets in this session will again follow along 0 s will fill in the rest of the third column MCW AFNI 2 00 10 Dec 30 1996 kkk gt afni im For this to be possible it is necessary that the correct geometrical relationship between the datasets comprising a session be established when to3d is run that is the import of getting the axes orientations and origins correct in to3d AFNI is also capable of directly reading in and displaying a set of image files Use the command afni help for detailed instructions on how to do this In this mode none of the controls for dataset transformation functional overlay etc are available After you start AFNI a control window opens on the X11 screen JA AFNI sample96 anattorig amp vi tsloperorig a 4 400 mm CRI Original View 1 406 mm P AC PC Aligned 1 406 mm I g A i x Talairach Yiew Norm IColr Swap Xhairs Multi 5 a i Define Markers c Color green ff b i
9. between vertical grid lines in time steps is shown in this case there is a grid line every 10 time step The Num label shows the number of points in the time series At the bottom of the graphs is a label starting with index This shows the time index of the current point which can be altered with the control on the AF NI controller window the value of the time series at that point and the time coordinate of that time index in this case 211 25 seconds The current time point is displayed with a little red ball overlaid n the central sub graph in the figure above red is rendered in gray At the left of the graphs are two numeric labels in this case 802 and 891 802 89 This shows the vertical range of the central sub graph In this display each sub graph has its minimum point at the bottom of its sub window Every sub graph has the same vertical scale factor but has a different vertical offset This is so that they will all fit in the same display easily This can be confusing when comparing levels of adjacent pixels it is important to realize that there can be an arbitrary constant offset between adjacent sub graphs The button on the menu can be used to ensure that all sub graphs are plotted with the same vertical offset 4 4 1 Button Clicks in a Graph At the lower left of the graph window is a logo whose main function is to remind you from which plane these graphs are drawn This can be suppressed for window snapshot pu
10. inferior point in one of the temporal lobes is the hardest to pick out In the tacpc tlrc transformation marker control panel a toggle switch labeled appears just below the button In the earliest ver sions of AF NI the brain data was clipped at 55 mm inferior to the AC PC line this being the location of the bottom of the Talairach Tournoux atlas figures In subsequent work we found this was inadequate for cerebellar imaging The new default clipping level is 65 mm MCW AFNI 2 00 29 Dec 30 1996 inferior to the AC PC line and this is referred to as the Big Talairach Box Datasets BRIKs created with the old small box size are smaller than the new box size There is no way to mix old and new box size datasets together when using the auxiliary analysis programs such as 3dANOVA For this reason and to maintain compatibility with old analyses it is possible to write out old box size dataset BRIKs by toggling this switch off For all future work I strongly recommend using the new Talairach box size The transformation carried out is precisely the one described in 1 and I recommend that anyone using AFNI read this atlas The dataset is divided into 12 subvolumes e In x Right to Midsagittal Midsagittal to Left e In y Anterior to AC AC to PC PC to Posterior e In z Inferior to AC AC to Superior Each region is scaled separately to match the millimetric coordinates in the atlas x axis AC PC line to most left point
11. kA a o o 2 z The actual implementation of interpolation is done in a somewhat different fashion for the sake of efficiency See the source code in afni slice c 7 Acknowledgements Many thanks to Jim Hyde for much support and many discussions on the direction of FMRI analyses Thanks also are due to Andrzej Jesmanowicz for forging the way with AFNI s grandfather FD Doug Ward has contributed a lot with the 3dfim and 3dANOVA programs new features in 3dmerge plus the creation of the auxiliary programs manual Mike Beauchamp has aided immeasurably by testing earlier versions of this software and by coming up with many useful ideas Jay Kummer contributed the initial idea for plugins Many other people at MCW have also helped particularly with quick questions you know who you are and the occasional warm pumpernickel bagel This work was partly supported by the United States NIH through grants MH51358 and NS34798 for which I am also grateful MCW AFNI 2 00 38 Dec 30 1996 References 1 Jean Talairach and Pierre Tournoux Co Planar Stereotazic Atlas of the Human Brain Thieme Medical Publishers New York 1988 2 Peter A Bandettini Andrzej Jesmanowicz Eric C Wong and James S Hyde Process ing strategies for time course data sets in functional MRI of the human brain Magn Reson Med 30 161 173 1993 3 Robert W Cox AFNI Software for analysis and visualization of functional magnetic resonance
12. neuroimages Computers and Biomedical Research 29 162 173 1996 4 Robert W Cox Andrzej Jesmanowicz and James S Hyde Real time functional mag netic resonance imaging Magn Reson Med 33 230 236 1995 MCW AFNI 2 00 39 Dec 30 1996 Disclaimer MCW AFNI its associated programs and its documentation are provided as is and no warranty for their correctness or usefulness for any purpose is made or implied by the Medical College of Wis consin MCW or by the author of the software Neither MCW nor the author accepts any liability for any defects in this software or its manuals or for any damages caused by use of this software Ownership Conditions of Use and Restrictions e Permission is granted to make use of and to make copies of the MCW AFNI software and documentation for non commercial research purposes only Ownership of MCW AFNI and all copies is retained by the Medical College of Wisconsin e Patient care applications are not recommended MCW AFNI has not been evaluated by or approved by the United States Food and Drug Administration e Use for any purpose by for profit organizations is prohibited without prior arrangement and written permission e Redistribution of MCW AFNI or any derived work outside the receiving institution is prohibited without prior permission e Copies may be made within the receiving institution without separate permission from the Medical College of Wisconsin e Technical support
13. of cerebrum 68 mm x axis AC PC line to most right point of cerebrum 68 mm y axis Most anterior point of cerebrum to AC 70mm y axis AC to PC 23 mm y axis PC to most posterior point of cerebrum 79 mm z axis Most inferior point of cerebrum to AC PC line 42 mm z axis AC PC line to most superior point of cerebrum 74 mm The atlas brain is from an adult female and so a typical adult male brain will be slightly compressed by these standard measurements Any jokes at this point will be sternly dealt with This transformation is then combined with the orig gt acpc transformation so that the data viewed in the Talairach mode is only interpolated once not twice The whole procedure to produce the tlrc view from the orig view only takes a few moments once you become adept at recognizing the requisite anatomical landmarks You will find that the marker toggle buttons and set clear buttons are duplicated on the popup menu from the imaging windows This is for convenience since it is often necessary to peer closely at the screen to decide on a marker point and I personally find it annoying to have to switch my attention to another window in order to set the marker Also note that depressing the toggle button in the marker control column or on the popup menu for an already set marker will cause AFNI to jump the crosshair viewpoint to that marker location Finally note that there are no markers available to be set in the Talaira
14. of view then the saved image aspect ratio will be distorted The only way to rectify this in AF NI is to switch the dataset to be warp on demand using the Datamode controls which always interpolates to square pixels To actually save the pixels as displayed on the screen some sort of snapshot or window grab utility is needed If none other is available the shareware program xv has a window grab function Or the xwd command line program can be used with appropriate conversion using the netpbm utilities For example the images displayed in this manual were captured with variants of the following command line xwd frame xwdtopnm pnmdepth 255 ppmtopgm pgmnorm pnmtops noturn gt name eps 4 3 6 control This button allows you to make a montage of more than one slice in the image window It pops up a control panel pictured earlier and below For convenience in programming only one of the and control panels can be open at a time per image viewer This restriction may be lifted in some later version of AFNI but no guarantees MCW AFNI 2 00 16 Dec 30 1996 A AFNI verbal anat tire amp fnew 1234 tIre Montage Controls Across 3 Down Spacing ior Border Oom Color gry bb oO fouit 1x1 Draw Set Example of slice montage with control panel The five montage menu controls from top to bottom are This controls the number of slices to be displayed horizontally across the win dow
15. one of the Run buttons 3D Cluster AFNI Plugin Dataset Clustering Quit Run Keep Run Close Help _ BD Function verbal r4 time 1 ori E EEE Radiuscnm FF 1 6 E Minvol ul FF 1000 E Threshold cutoff aa 10 5 Clustering plugin plug_clust c interface panel 5 Command line switches The general form for the AFNI command line is afni options session_directory where the options listed below all start with the character If no session directories are entered then the program acts as if the user had typed for the session which means that the current working directory will be scanned for datasets What I consider to be the more useful options are listed below A complete list can be found by entering the command afni help e purge Conserves memory by purging datasets to disk when not in use Use this if you run out of memory when running AFNI This will slow the code down so use only if needed Another application for the purge switch arises when using Unix symbolic links to make a dataset appear as if it is in more than one session directory at once without copying the brick file For example suppose one creates using 3dmerge an averaged MCW AFNI 2 00 35 Dec 30 1996 anatomical dataset GRP tlrc HEAD and GRP tlrc BRIK from sessions fred ethel and lucy This could be done from the directory above the sessions by the commands 3dmerge prefix GRP gmean anat
16. systems e SGI Indigo workstations R4400 and R10000 CPUs running IRIX 5 3 and IRIX 6 2 e HP 9000 735 workstations running HP UX 9 05 e Intel based Linux 1 2 13 systems e Sun SPARCstations running Solaris 2 5 It has not been tested on other platforms It will not work with X11R4 or Motif 1 1 in particular it does not work under SGI IRIX 4 x There are no plans to port it to radically different platforms such as Microsoft Windows or the Apple Macintosh AFNI is a powerful program for display and manipulation of functional neuroimages with many options Study of this manual and experience with the program are both required to make full use of AFNI Some experience with using X11 is also very useful and will be assumed in this manual Nomenclature In general I refer to MCW AFNI as the whole software package The particular program AFNI is at the heart of the package and is the subject of this manual The package includes a number of other programs and the programming interface for creating plugins both of which are documented elsewhere If you find MCW AFNI useful and wish to refer to it in a publication the appropriate citation is 3 MCW AFNI 2 00 3 Dec 30 1996 What s New Atomic Datum Types Previously the data stored in an AFNI dataset had to be 16 bit signed integers short datum The new dataset format allows for 8 bit unsigned integers byte datum 32 bit floating points numbers float datum
17. that you use the C shell csh or its superset tcsh I said above that time series files are stored as one number per line This is true of the older programs such as fim2 FD2 etc but AF NI itself allows more than one number per line In this way more than one time series can be stored per file 99999 99999 99999 99999 99999 99999 99999 99999 0 0 0 0 10 0 0 0 10 10 0 0 0 10 10 0 0 0 10 10 10 0 0 10 10 10 0 0 The above example defines four time series in one file Each one starts with two 99999s which indicates that these two points should not be used in any analysis with these time series The subsequent values could be used as an ideal waveform in FIM analysis In this example each timeseries after the first is a time delayed copy of the one to the left A Unix command of the form pr m t s a 1D b 1D c 1D d 1D gt abcd 1Dx MCW AFNI 2 00 23 Dec 30 1996 can be used to glue multiple files together horizontally into a single file with multiple columns You should be sure that all the files have the same number of lines before using the pr command which is really a program designed for formatting files for printout On SGI workstations the pr command has a small upper limit to the number of columns it will output On such systems it may be necessary to paste up a large number of columns in two stages To allow such time series files to be distinguished from ordinary files containing only one t
18. the appearance of the graphs This is a pullright menu used to control the vertical scale of the graphs The figure above shows the sub menu that results from pulling right on this item The and buttons will cause the graphs to scale down shrink and up grow Pressing the keys and in the graph window will have the same effects The button will cause a little chooser to popup which allows you set the vertical scale factor manually If the scale factor is positive then it is the number of screen pixels to use per unit of data If the scale factor is negative its absolute value is the number of units of data per screen pixel Thus increasing the scale factor will cause the graph to grow vertically There is no provision in AFNI for automatic scaling to fit the dataset range each graph window starts with its scale factor set to 1 Judicious use of the or keys may be needed to make a graph visible This pullright menu is used to control the number of sub graphs displayed It shows a sub menu similar to the sub menu In this case keystroke m will cause the number of sub graphs displayed across and down to decrease by 1 keystroke M will increase the array size by 1 will let you directly set the number of sub graphs This pullright menu lets you control the spacing in time steps between vertical grid lines This pullright menu lets you move the spatial viewpoint between slices in the data
19. tote y 33 ig A 8 ass Soin O s 4 2 Program Control 11 Re Ee fadei J 4 3 Image Display a 12 5 Command line switches 35 4 3 1 Crosshairs and the View PONG o de g h e 12 6 Technical Notes 37 4 3 2 Colormap Controls 13 6 1 mmap ing 37 4 3 3 Position Controls 14 6 2 machdep h onana aaah 38 4 3 4 Disp Control 14 6 3 X11 Resources for AFNI 38 4 3 5 Bave Control 15 6 4 Formula for Bk Resampling 38 4 3 6 Mont control 16 4 3 7 Popup Menu 18 7 Acknowledgements 38 4 3 8 Resizing Image Windows 19 4 4 Graph Display 19 Hieterenees K 4 4 1 Button Clicks in a Graph 20 MCW AFNI Registration Form 40 4 4 2 Opt menu 21 4 4 3 EIM menmu 22 4 5 Viewing Controls 26 4 5 1 View Modes 26 4 5 2 Define Controls 27 4 5 3 Switch Controls 27 4 6 Define Markers 27 4 6 1 Markers for the AC PC Aligned Transformation 27 4 6 2 Making the Transforma Hon e re wee Se sh 29 4 6 3 Transformation to Stereo taxic i e Talairach Co ordinates 29 4 6 4 Re transformation and Re creation of Datasets 30 MCW AFNI 2 00 2 Dec 30 1996 kkk Whats New kkk Computer requisites 1 Introduction AFNI is an interactive program for viewing the results of 3D functional neuroimaging It can overlay the usually low resolution results of functional brain scans onto higher resolution structural volume data sets By mar
20. 0 17 Dec 30 1996 KkKkK gt Seeing individual voxel values This will instruct the image viewing window to redraw itself as currently com manded This button will display in inverted colors until the redraw operation is complete If the dataset is warp on demand and many slices are requested this operation may take several seconds This combines the functions of and Quit it will redraw the window as commanded and also close the control panel Slices are displayed starting in the upper left corner then from left to right then top to bottom If the controls are used to rotate or mirror the images these operations apply to each slice individually not to the montage as a whole If the number of slices displayed Across x Down is large and Spacing is large then the extreme slices requested may be outside the dataset In such a case the toggle on the AF NI controller window next to the menu controls what happens If is turned on then slices requested past the edge of the dataset will be wrapped back to the opposite edge If is turned off then slices requested past the edge of the dataset will be filled with zeros The only slice image which will have crosshairs displayed is the one containing the current viewpoint Clicking mouse Button 1 in any slice image will cause the current viewpoint to jump to that location in that slice This will also cause that slice to jump to the center position in the montage layout If t
21. IM computations compute the correlation coefficient of each voxel with each column separately Then the column that is most highly correlated with the voxel time series is selected to compute the a for that voxel becomes the intensity and the correlation coefficient becomes the second sub brick stored in the resulting fico dataset MCW AFNI 2 00 24 Dec 30 1996 When the ideal time series is selected it will be plotted at the top of the center sub graph window in red Sections of it that are marked to be ignored will be plotted in blue If there is more than one column in the ideal time series by default they will all be plotted By the way the button on the time series chooser is permanently deactivated I intended to provide the ability to preview a time series in a little window but never got around to implementing it The button remains to remind me of this and to remind me of all my other goals for AFNI that have yet to come to fruition In the mathematical model for n given earlier note that we included a bn in the model to represent the unknown baseline and drift of the data time series These are orts time series to which the data time series is orthogonalized prior to the correlation coefficient calculation 4 AFNI always orthogonalizes the data to these two time series In addition you may specify another time series to which the data time series in each voxel should be orthogonalized If the ort time s
22. In the example above Across and Down are both set to 3 This controls the number of slices to be displayed vertically down the window This controls the frequency with which slices are displayed Spacing of 1 means that adjacent slices will be displayed 2 means that every other slice will be displayed etc The units of this selector are slices not millimeters thus changing the resolution of a warp on demand dataset using Datamode controls will change the inter slice distance as displayed here In the example above the images are 10 slices apart Since this is in the Talairach view which can be seen from the dataset names in the image viewer titlebar and the default voxel size of 1 mm was used these sagittal slices are 10 mm apart center to center This controls the thickness in dataset pixels not screen pixels of the border to draw between slice images In the above example this is set to 3 This controls the color of the border drawn between slice images In the above example this is set to a gray color under the presumption that you do not have a color PostScript printer with which to output this manual Across the bottom of the control panel are four action buttons Their functions are This will close the control panel and leave the current montage layout unchanged This will reset the and controls to each be 1 This is simply a convenience for when you wish to go back to displaying a single slice MCW AFNI 2 0
23. Internally AFNI uses DICOM coordinates to keep track of everything However AFNI cannot read DICOM files The button just under the coordinate display allows you to switch between 3 modes for crosshair display Crosshairs are not displayed A single crosshair is displayed at the x y z coordinates of the viewpoint i e the point whose coordinates are given in the upper left corner If a montage of slices is displayed in an image viewing window then the orthogonal slices will have crosshairs indicated for all the montaged slices This is useful for indicating the anatomical location of the montage layout You may change the crosshair color and central gap with the selectors just underneath the button The colors available for the various overlays are built into AFNI but can be altered by appropriate changes to your Xdefaults file If you click the left mouse button while the cursor is in an image window then the crosshairs will immediately jump to that location This will usually mean that the other two windows will display new slices The image windows are always linked in this fashion The control on the AFNI controller window is used to control the time index of the viewpoint This control is only active if the current anatomical dataset is in the 3D time format The time index can also be controlled in a graph viewer 4 3 2 Colormap Controls At the right of each image window is a set of buttons that are used to
24. MCW AFNI User Manual Medical College of Wisconsin Analysis of Functional Neurolmages Version 2 00 December 1996 Robert W Cox Ph D Biophysics Research Institute Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee WI 53226 1996 Medical College of Wisconsin Summary MCW AFNI displays three dimensional functional neuroimages overlaid onto anatomical reference scans Data may be transformed to the Talairach Tournoux stereo taxic proportional grid system Images may be generated in each of the three cardinal orthogonal planes and switched among multiple functional anatomical data volumes Aux iliary programs are provided to manipulate and combine 3D image sets Time dependent 3D image sets may also be stored displayed and manipulated An application programmer interface is provided to allow users to extend the functionality of AFNI via plugins Document This manual describes the use of the AFNI program version 2 00 Earlier versions 1 xx are superseded by this version bugs in the earlier programs will no longer be fixed Separate manuals are provided for the auxiliary programs and for the program ming of plugins Disclaimer This software and its associated manuals are provided AS IS and no warranty for their usefulness or correctness for any purpose is made or implied by the Medical College of Wisconsin or by the author This software has not been approved or evaluated by the United States F
25. Pbar The multi colored vertical bar with numerical labels to the right and a number selector labeled below is called the pbar after its name in the C code This device controls the colors for the functional overlay The number selector beneath the pbar control how many color panes are present from 2 to 10 are available the default in AFNI is set to 9 panes Just below that is a toggle switch Pos This allows you to specify that only positive values will the shown in the color pbar or that both positive and negative values will be shown Some functional datasets are naturally nonnegative for these allocating colors to the negative range is pointless The color in any pane may be altered by clicking inside the pane itself A chooser will then popup to let you select from the available palette which is hard coded into AFNI and can only be changed via the Xdefaults file One color choice is none which means that no color will display for that range of functional intensities even if they appear in voxels that are over the selected threshold Each color pane applies to the indicated range of functional intensities These intensities are relative to the Range control settings to the lower right The Range setting is is mapped to 1 0 on the pbar and all other pbar settings correspond to the similarly scaled values in the functional dataset sub brick being viewed You may click and drag on the sashes between the
26. and or X terminals Several Makefiles are included in the distribution The machines they are intended for are indicated by their filename suffix In general you will have to modify one of these to fit your needs You may also need to edit the file machdep h to set up the flags for the mmap routine appropriately Copy the appropriate file to be Makefile Examine it to make sure that it makes sense on your system To build the executables use the command make all If you set the INSTALLDIR macro correctly in the Makefile then make install will mv the executable images to their final resting spot After that a make clean is appropriate To make and install the plugins supplied with AF NI the commands make plugins and make install_plugins will work Not all system specific Makefiles have the commands needed to compile plugins This is because I do not have access to such computer systems There are undoubtedly still bugs in this software Suggestions for further improvements will be gladly received but no action on such suggestions can be guaranteed The e mail address for AFNI comments is rwcox mcw edu 6 1 mmap ing AFNI uses the Unix function mmap to access the BRIK files This is what makes it possible to read in many large datasets and not choke the memory or swap space of the computer Data is only read from disk using mmap all writes are done using fwrite If you need to disable the use of mmap edit the file 3ddata h and def i
27. ch view mode At present there are no transformations beyond this one maybe someday 4 6 4 Re transformation and Re creation of Datasets If you decide to re mark and re transform an anatomical dataset then the old transformed version will be deleted from disk before the new version is made Not only that but all the automatically manufactured transformed datasets that follow on this transformation will also be destroyed and remade This can be disconcerting at first but it is the only logical course of action for AFNI to take otherwise the transformed functional datasets MCW AFNI 2 00 30 Dec 30 1996 would have been made with a different transformation than the new anatomical dataset on which they will be overlaid The only time this destruction is inappropriate is when the functional datasets in the transformed view are not in fact transformations from original datasets in the same session This could happen if you copied a tlrc dataset into a session from another directory or if you created a tlrc dataset using 3dmerge say AFNI will not delete a dataset if there is no parent dataset from which it was warped AFNI will not let you mark and transform more than one anatomical dataset per session Once you have transformed one dataset in a session the others will be off limits to direct marking and transformation Their transformations will be derived from the master dataset that you mark first Corr Inten Opt
28. color panes to change the intensity thresholds 4 7 3 Options The options column is a grab bag of functional dataset stuff The first boxed set of buttons Anat underlay etc lets you choose whether the anatomical dataset or the functional dataset appears as the background grayscale images in the viewing windows The second boxed set Func Intensityl etc lets you choose between displaying the intensity or the threshold as the color determining function The third boxed set comprised the range controls for the functional coloring At the top are the minimum and maximum values found in the current datasets cf auxiliary program 3dinfo The next control is a toggle labeled autoRange xxxx The value represented by xxxx is the automatically assigned range for the functional range which corresponds to 1 0 on the pbar This autoRange is chosen by AF NI as the largest absolute value in the dataset sub brick If the toggle is off then the control below is activated and allows you to specify the functional value that maps to 1 0 on the pbar Controlling this range may be desirable when comparing several datasets The lowest so far control in this column provides another menu button see the Graph section The label to the right of this button shows the dataset that will be processed once the Compute FIM button is pressed MCW AFNI 2 00 32 Dec 30 1996 KkKk Warp on demand subvoxel markers kkk Resampling mod
29. consultation with a neuroanatomy textbook will probably be helpful in learning to recognize the required anatomical landmarks 4 6 2 Making the Transformation When all markers are set the button will become active This button will check the marker set for elementary consistency If the markers don t pass the test an error message pops up to explain what happened If they do pass the test then the button becomes active When you press this the new dataset will be created in this case the acpc view of the anatomical dataset you were just marker ing This new dataset will not have a BRIK file on disk just a HEAD file When AFNI comes to display this dataset it will simply transform the needed data from the orig dataset If you wish you may save the data voxels in the new view to disk using the Datamode controls If you wish to manipulate a transformed dataset using the auxiliary programs you will have to save the data voxels to disk 4 6 3 Transformation to Stereotaxic i e Talairach Coordinates After you create the AC PC aligned view you can switch to it with the AC PC Aligned button At this point you can set markers for the scaling to the Talairach view Six markers are required to define the bounding box of the cerebral cortex These should be set quite carefully since it is often easy to mistake the sagittal sinus for cortex which would give an erroneously large box in the z direction Generally I find that the most
30. control the X11 colormap assigned to the windows From top to bottom these controls Change from grayscale to a colorscale and back g 8 Invert the grayscale or colorscale swap it end for end Return the colormap to its initial state after you mess it up Change the contrast of the grayscale a multiplicative change to the intensity of each pixel b Change the brightness of the grayscale an additive change to the intensity of each pixel Rotate the grayscale or colorscale Change the y correction factor for the grayscale amp 2i MCW AFNI 2 00 13 Dec 30 1996 Change the fraction of the viewing window taken up by the image You may have to drag the viewing windows to be larger than their initial sizes so that these and the other controls don t obscure each other Changing the colormap in one viewing window affects all the other windows from the same AF NI process 4 3 3 Position Controls Below each image is a slider that indicates the image number in the current sequence By dragging this slider you can move through the slices to any given slice number In doing so you will also move the crosshairs in the other two image windows At the lower right of the image window is an arrowpad of four arrows arranged in a N E W S pattern plus a central button Clicking on one of the arrows will cause the crosshair viewpoint to move one voxel in the direction pointed by the arrow in that window Clicking on the cent
31. e g the fixing of bugs for MCW AFNI is not guaranteed I agree to abide by the terms and restrictions above SIGNATURE NAME print clearly or type DATE E MAIL ADDRESS print clearly or type To Register Copy this page onto your departmental or institutional letterhead sign and date include your e mail address and return via mail or FAX to Robert W Cox PhD Biophysics Research Institute Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee WI 53226 USA FAX 414 456 6512 Instructions on how to obtain AFNI by anonymous ftp will be sent by e mail MCW AFNI 2 00 40 Dec 30 1996
32. e their locations and sizes is that it is often desirable expand one window to look at some details and temporarily cover up the other windows When an button is highlighted in inverted colors this means that its window is al ready open Pressing the button again will bring that window to the top of the display this is useful if the image viewing window is hidden beneath some other window or is iconified An image viewing window can be closed by using the button along its bottom edge Alternatively the window manager Close or Delete function may be used 4 3 1 Crosshairs and the Viewpoint You can have up to three image viewing windows open at any given time one axial one sagittal and one coronal In the axial and coronal windows images are displayed with the subject s left on the screen right the usual radiological convention These windows are orthogonal slices through the 3D dataset The colored crosshairs that overlay each image mark the slices that are visible in the other image windows The point at which the crosshairs intersect is called the viewpoint In the upper left hand corner of the AFNI controller window are displayed the coordinates of the current viewpoint These coordinates are presented in the DICOM 3 0 standard order x axis is Right negative to Left positive MCW AFNI 2 00 12 Dec 30 1996 y axis is Anterior negative to Posterior positive z axis is Inferior negative to Superior positive
33. e used to select active voxels at a given significance fift Functional Intensity F test e two values are stored per voxel e the first is intensity e the second is an F statistic which can be used to select active voxels at a given significance By intensity I mean a signed number indicating the level of functional activity in each voxel I consider the fith dataset type to be obsolete It is retained for compatibility with AFNI version 1 0x The latter three functional types differ from the fith type in that AFNI knows how to statistically interpret the second value attached to each voxel The values stored at each voxel can be any of the following byte a typedef for unsigned char short 2 byte signed int float single precision 4 bytes complex a struct containing two floats 8 bytes I refer to these types as the atomic datum types of a dataset Float and complex datasets may not be portable between CPU architectures Also short datasets may need to be byte swapped if the files are moved to a different computer Specifically Intel CPUs are reversed from most other Unix systems so that short brick files created on an SGI system would have to be byte reversed before they could be used on an Intel based system The auxiliary program 2swap can perform this function For most purposes the short atomic datum is the most useful Each 3D brick within a short or byte dataset can have a floating point sca
34. eries Files MCW AFNI stores single time series such as r in the format described earlier ASCII format one number per line A number greater than 33333 0 means that particular point in time should be ignored This convention goes back to the original fim program in 1990 and is due to Andrzej Jesmanowicz of MCW The button described above is one way to create such a time series file Another is with the auxiliary program sqwave Yet another is simply to use a text editor such as vi When AFNI starts up it will read in time series files from the session directories that it opens The program will attempt to read a time series from any file whose name ends in 1D These time series will be pooled into a library whose entries can be selected from a menu as described below You may wish to keep some time series files stored separately from any particular session directory AFNI can be made to read such files by defining the shell environment variable AFNI_TSPATH Like the executables variable PATH this is a colon separated list of directories in which to search for particular files in this case 1D files For example setenv AFNI_TSPATH HOME timeseries will cause AFNI to search for time series in the timeseries directory under your home directory and in the current working directory Normally you would put this type of command in your cshrc file so that it would always be executed when you login I m assuming
35. eries has more than one column each data time series will be orthogonalized to all columns prior to the correlation coefficient calculation When the ort time series is selected it will be plotted in the middle of the center sub graph window in green Sections of it that are marked to be ignored will be plotted in blue Edit Ideal This pullright sub menu shown in a figure far above is used to control the ideal waveform The menu sub items are e Ideal Center will take the central sub graph data time series and make it the ideal time series e Ideal Center will take the central sub graph data time series and average it into the ideal time series In this way it is possible to select a group of voxels one at a time and average them together to make a single waveform e Smooth Ideal will apply a 3 neighborhood order statistics filter to smooth the current ideal waveform If the 3 points input are a b and c then the output is Yn 0 70 median a b c 0 15 max a b c 0 15 min a b c will popup a control panel that allows you to generate shifted copies of the current ideal waveform All the shifted copies form a multi column time series In this way it is possible to construct a single column ideal waveform use AFNI to create time shifted copies of it and then correlate them all with the data picking out the best time shift at each voxel will clear the current ideal waveform that is the
36. es 4 8 Define Datamode This control column determines how datasets are manipulated by AFNI It also contains some miscellaneous controls that didn t fit in elsewhere 4 8 1 Resampling The top boxed set of controls lets you choose how the anatomical data that is actually dis played will be generated You can view the data directly from the BRIK file if it is available In this case you are limited to seeing the dataset at the voxel resolution at which the data was generated Alternatively you can choose viewing which means that the data will be interpolated from its source to whatever resolution you order using the controls just below In this way it is possible to place markers at subvoxel locations At present AFNI cannot display graphs from a warp on demand dataset If you take an action that causes a 3D time dataset to be switched to warp on demand mode then any open graph windows will be destroyed This will happen for example if you switch from orig to tlrc view and have not yet written the 3D time dataset to disk The interpolation modes are nearest neighbor NN linear Li cubic Cu and blocky Bk this latter is intended mainly for functional datasets and is intermediate between NN and Li its mathematical definition is at the end of this manual NN Li and Bk are fairly rapid on a decent workstation but Cu can be noticeably slow Since it uses 64 neighboring grid points to i
37. f you save several functional datasets in the Talairach view mode using the Datamode controls then combine them with 3dmerge the result will only exist in the tlrc view You can only view this functional dataset when the view mode corresponds so the program will jump to that mode If such a view mode switch occurs the program will beep when it makes the transition 4 6 Define Markers The transformation to the AC PC aligned view and from there to the Talairach view is accomplished by means of markers These are anatomical landmarks that you manually select using the control column opened up by this control Only 3D anatomical datasets can have markers set 3D time datasets have the markers disabled It is only possible to transform a 3D time dataset to Talairach coordinates using a parent 3D dataset as described earlier the X s and 0 s diagram 4 6 1 Markers for the AC PC Aligned Transformation The AC PC aligned view mode is defined by a rigid body transformation that makes the AC PC line the new y axis makes the longitudinal fissure the new xz plane and makes the line perpendicular to that the new z axis right to left The new origin is put at the intersection of the AC PC line and the vertical line passing through the posterior margin of the AC See 1 for details MCW AFNI 2 00 27 Dec 30 1996 i 0000 yy i Corpus Callosum Pa Pineal i 7 Column of wy il Fornix Posterior
38. g Button 1 inside the help window will dismiss it Button help is implemented as a help callback in Motif If your terminal keyboard is appropriately set up then pressing the Motif Help key often F1 while the mouse cursor is over a button or other widget will also cause the help window for that widget to popup This button will close the controller window when pressed twice within 5 seconds If this is the only controller window running AFNI will also exit For more details try using on done The MCW logo will appear in the empty space just to the right of these four buttons when the program is doing some operation that is potentially time consuming At the same time the mouse cursor will change to a watch shape When the time consuming operation is over the logo will be removed and the cursor will change back to its usual arrow shape A trick I sometime use to visually grab attention when a lengthy task is underway is to click the button in an image window This will turn the images to reverse video when the program catches up with you Then again and proceed 4 3 Image Display The first column of the controller window contains the controls that enable you to open the image viewing windows the three buttons The windows open separately on the X11 display screen and may be positioned and resized independently A little practice is needed to decide upon a good layout scheme for these windows The reason AFNI does not defin
39. he button is set to Multi then orthogonal image viewing windows will show crosshairs for each slice drawn in the montaged window The only way that AFNI provides to save a montage display to disk is the function described earlier This function as all Save functions saves the image at its natural size one output pixel per dataset pixel regardless of any window resizing you may have imposed 4 3 7 Popup Menu If you click and hold mouse Button 3 usually the rightmost button while the cursor is in an image window a menu will popup at that point The first item on the menu is Jumpback This will reset the crosshair viewpoint to the last location clicked upon The main use of this feature is to recover from accidentally clicking Button 1 in an inconvenient location The second item on the popup menu is Jump to This will popup a window in which you may enter the x y z coordinates DICOM order of the point to which you wish to set the crosshair viewpoint One application the cluster locations reported by 3dclust may be pasted into the window The third item on the popup menu is Image display This will collapse the viewing window to just include the image Selecting this item again will bring the viewing window controls back One application making snapshots of nice functional displays N B This function does not work well on all X11 displays for unknown reasons It may collapse the image window to zero size which is s
40. he filename prefix for the slice data If you enter fred for the prefix then the 238 slice would be named fred 0238 pnm After you type in the desired prefix you click the button and then must choose the first and last slice indexes for the save operation from the new choosers that will popup When you the last slice index the write to disk operation starts Save bkg This form of the Save function is selected by toggling off the and options on the control panel In this form the action is to save the background image pixel values This does not mean the grayscale intensities displayed in the window It means that the actual values stored in the dataset BRIK file will be written to disk This button operates similarly to the function you must choose a filename prefix and the first and last slice indexes for the save operation If is selected on the control panel then the saved images will be expanded to the next largest power of two Using the Function controls you can switch to have the function displayed as the background In that way the functional dataset voxel values may be written to disk in slice format Alternatively the auxiliary program from3d can be used to write slice image files out of a dataset For all Save options the actual size of the displayed window doesn t matter the images saved to disk will reflect the voxel dimensions of the dataset In particular if the dataset voxels are not square in the plane
41. ideal waveform will be undefined after this is pressed The graph of the ideal waveform will also be cleared will clear the current ort waveform e Read Ideal allows you to read in the ideal waveform from an external file MCW AFNI 2 00 25 Dec 30 1996 e Write Ideal allows you to write the current ideal waveform to disk In this way an ideal created from the current dataset can be saved for later analysis allows you to store the current ideal waveform into the AFNI menu for possible later selection The only way to create an ort from a dataset is to first create it as an ideal then to store it with this button and then to use to get it off the time series menu The Write and Store operations are independent writing to disk does not imply storing in the menu system or vice versa This pullright menu allows you set the number of points to be ignored at the beginning of each time series This is often desirable since in rapid scan MRI the longitudinal magnetization may take several images to reach steady state Time points that are ignored either through the use of this control or large values 33333 in the ideal waveform will be skipped in the correlation analysis In addition points that are ignored with this control will not be graphed This allows large initial transients to be suppressed and makes it easier to read the graphs This pullright menu allows you to specify whether all the columns of the ideal
42. iginal left and AC PC Aligned right Control Panels MCW AFNI 2 00 28 Dec 30 1996 kkk gt Sub voxel marker locations You select a landmark by depressing its button then moving the crosshairs to the desired location then clicking the button A visible marker will appear You can reset this point or it When a marker is set its toggle button will appear in inverted colors The atlas definitions of the marker locations are always in terms of a boundary That is slightly ambiguous when it comes to discrete images do you mark the last voxel visible in the structure or the first voxel just outside the structure My arbitrary solution to this problem is always to mark the last voxel visible in the structure For example in marking the top of the AC I move up until it is just no longer visible in the axial image Then I drop back down one axial slice It is possible to use warp on demand to place markers at subvoxel locations see the Datamode controls On MR images with 1 mm voxels and with good gray white matter contrast it is usually quite easy to set the AC markers At MCW we use a GE Signa SPGR sequence for this purpose The PC is harder to spot but it is always near the top of the cerebral aqueduct in subjects with normal anatomy it might be displaced by some pathological conditions if you suspect this has happened consult a neuroradiologist immediately Examination of the sample AFNI dataset and some
43. images are clipped to the known dimensions of human MCW AFNI 2 00 26 Dec 30 1996 heads This is to save space when such datasets are written to disk The window resizing is set up to preserve the pixels per brain millimeter ratio The program also attempts to keep the crosshair viewpoint in the same anatomical location as they were in the previous view mode but they may shift slightly Since the torig view will generally be rotated from the tacpc and tlrc views keeping the viewpoint at the same location does not mean keeping the slices in the same location 4 5 2 Controls Each button opens up another control panel to the right of this second column They are discussed separately later Note that to close a Define control panel you press its button again To help with this the buttons that are currently open are displayed in inverted colors You may open more than one Define control panel at a time but they will all lie on top of each other most recently opened panel on top 4 5 3 Controls These controls let you choose which session and which datasets from that session you are viewing at any given moment They popup a chooser that lets you cycle between the session directories the anatomical dataset prefixes and the functional dataset prefixes respectively When you switch datasets AFNI may be forced to switch views as well This can occur if the new dataset doesn t exist in the view mode you were formerly in For example i
44. ime series AFNI allows the use of the filename suffix 1Dx as in the pr command example above However there is no difference between the 1Dx files and the 1D files as far as AFNI is concerned it is perfectly acceptable to have a multi column time series filename end in 1D or to have a single column time series filename end in 1Dx At this release only the actual AFNI program will recognize these multi column time series files correctly Other programs such as fim2 still require each file to contain only one time series Choose One FIM Reference Yector timeseries cos6 25 1D timeseries cos6 50 1D timeseries cos6 75 1D timeseries cos7 00 1D timeseries cos7 25 1D timeseries cos7 50 1D timeseries cos7 75 1D timeseries cos8 00 1D timeseries cos8 25 1D timeseries cos8 50 1D timeseries cos8 75 1D timeseries cos9 00 1D timeseries cos9 25 1D timeseries fred 1D timeser ies qqq 1Dx timeseries ref400 1D x x KX KKK KX KX KK K K XK Sample time series chooser menu Menu Items Pick Ideal This button pops up a chooser window which allows you to select a time series file to be used as the ideal waveform r an example of this chooser is shown above With each time series filename is shown the dimensions of the time series In the example the file qqq 1Dx has 68 points in time 68 lines of data and has 13 columns If the ideal time series has more than one column the F
45. ions Anat underlay A Func underlay Func Thr underlay View Anat Data Brick Warp Anat on Demand Anat resam mode Li m Resam Cm fr x i 4 Func Intensity A Func Threshold Anat 0 857 Func 0 020871 0 024135 Thr 0 5906 0 5689 E autoRange 9 024135 FIM viztimetorig Warp Func on Demand Func resam mode NN i Many Rescan This jar 1D Lock Plugins Define Function and Define Datamode control panels 4 7 Define Function The buttons and other widgets on this control panel are used to manipulate how functional datasets are displayed in the viewer windows 4 7 1 Threshold Slider If the current functional dataset has a threshold data sub brick i e is not of the fim type then the first item in the Function control panel is a slider that lets you select the threshold to apply Only voxels whose associated value is equal to or above this threshold will be overlaid in color If the functional dataset type is fico fitt or fift then AFNI knows how to interpret the threshold level in terms of the standard normal models for these statistics and will show the corresponding p value per voxel just below the slider The dataset threshold type is shown at the top of the slider MCW AFNI 2 00 31 Dec 30 1996 If the functional dataset is of the fim type then this slider will not be visible In this case the leftmost item in the Function panel will be 4 7 2 Color
46. ire filesystem hierarchy from each session_directory given on the command line On a large disk this may take a long time To limit the recursion to 5 levels for example use R5 e ignore N Tells the program to ignore the first N points in time series for graphs and FIM calcu lations e unique Tells the program to create a unique set of colors for each AFNI controller window This allows different datasets to be viewed with different grayscales or colorscales unique will only work on 12 bit PseudoColor displays for example SGI workstations MCW AFNI 2 00 36 Dec 30 1996 e ncolors nn Tells AFNI to use nn gray levels for the image displays default is 80 Since AF NI always uses the default colormap on a 8 bit graphics system you may run out of colors if you run several graphics programs at once WWW browsers are notorious for causing this problem since they usually allocate many colormap entries and hold onto them just like AFNI does 6 Technical Notes The MCW AFNI package is distributed as a compressed Unix tar file afni96 tgz It is unpacked with the command gzip dc afni96 tgz tar xf The files will go into a directory named AFNI96 AFNI requires an ANSI C compiler X11R5 and Motif 1 2 It also requires that the default X11 Visual be an 8 or 12 bit PseudoColor visual the program will not work with anything else This is ordinarily not a problem except on very low end and very high end workstations
47. king fiducial points you may transform the data to the proportional grid stereotaxic coordinates of Talairach and Tournoux 1 Time dependent 3D volume data sets can also be created and viewed Auxiliary programs are provided for combining and editing 3D and 3D time functional data sets With this new version of MCW AFNI my intention is to add many new analytical capabil ities to the software system Some of these are found in the auxiliary programs Others are found in the AF NI program itself in particular the interactive ability to compute functional activation using the correlation method 2 The new plugins capability offers C literate users the ability to integrate their own analytical tools into AF NI It is my hope that other sites will develop AFNI plugins and share them with the FMRI community This document has been extensively rewritten from the version 1 0x manuals Major new facilities in AF NI are outlined in the next section The program runs on Unix workstations using the X11 windowing system and the Motif 1 2 toolkit for its graphical interface Minimum system requirements to use AFNI are 32 MB RAM 64 128 MB will work much better X11R5 with Motif 1 2 an ANSI C compiler and enough disk space to hold the 3D data volumes required AF NI is designed to work with 8 or 12 bit PseudoColor X11 visuals A visual of this type must be the default visual on the system used to display AF NI The program has been tested on the following
48. l be used Command line options for AFNI will be discussed in a later section For AFNI to be able to use a session it must contain at least one anatomical dataset 3D or 3D time If none are available the auxiliary program 3ddup can be used to create a warp on demand copy of a functional dataset Alternatively you could use the first image from the FMRI time course in each slice to form an anatomical dataset but a separate higher resolution scan will be more useful and look better At any given moment in AFNI you are viewing one given anatomical dataset and possibly one given functional dataset Controls are supplied to let you switch among sessions and among datasets within sessions A useful model is to think of each session as being organized in a two dimensional layout So SSo4s5 View Type orig acpc tlrc anat X X prefix angio X 0 funci X 0 func2 X 0 Across the top is the view type Original AC PC aligned or Talairach Down is the dataset prefix X s mark datasets that actually exist on disk In the sample above the anat original data has also been transformed to the AC PC aligned view using the marker driven transformation described later When AFNI starts all the other datasets in this session will also have AC PC aligned view versions made internally in the program these are indicated by 0 s in the table above No HEAD files will be written for these datasets at this time These datasets will
49. lf can deal with warp on demand datasets That is all the auxiliary programs and plugins must deal with actual dataset BRIKs MCW AFNI 2 00 8 Dec 30 1996 KkK e gt Crucial information KkKk gt Command line names for sessions datasets 3 2 Sessions All of the dataset files that go together should be gathered into a single directory By go together I specifically mean those datasets gathered during the same scanning session on a single subject After their positions and orientations are set up in to3d all these datasets are presumed to be aligned to one another If this is not the case then the images making up the datasets should be registered before entry into to3d The auxiliary program imreg may be useful for this purpose Alternatively the program AIR from UCLA might be needed AIR is available at http bishopw loni ucla edu AIR index html A directory containing datasets is called a session The hierarchy of files that make up a session is pictured below session lt top level directory header header header lt actual data files brick brick brick header header header brick brick It is permissible to save other files e g the original image files in the session directory these files will simply be ignored by AFNI AFNI takes as input a collection of sessions specified by their directory names and allows you to switch between them and between thei
50. lightly inconvenient When all three viewing windows Axial Sagittal and Coronal are open the bottom item on the popup menu will contain a display of the background pixel value at the center of MCW AFNT 2 00 18 Dec 30 1996 the crosshairs The background is normally an anatomical image but can also be switched to be a functional image using the Function controls 4 3 8 Resizing Image Windows When a viewing window is first opened it is at the natural dimension for the resolution set in the Datamode controls or in the dataset header file if viewing from the data brick When jumping from one coordinate system to another or from one dataset to another the program attempts to keep the on screen pixels mm the same so that no sudden scale changes occur When the viewing windows are resized the images are stretched by nearest neighbor resampling This has nothing to do with the resampling modes set in the Datamode and Function controls For example the crosshairs are exactly one pixel thick in the natural dimension of each window If a window is stretched then the crosshairs will become thicker If a window is shrunk the crosshairs may disappear when they are missed during the display resampling When viewing from the data brick and when the data voxels are not cubical the viewing windows will similarly stretch the coarser direction to maintain the correct physical aspect ratio on the screen assuming that the X11 pixe
51. ling factor attached so that the AFNI programs will interpret the value stored as factor x vozel value MCW AFNI 2 00 7 Dec 30 1996 kkk File names kkk Warp on demand Datasets are stored in two files the header and brick files The header file contains all the auxiliary information about a dataset stored in an ASCII format The brick file contains only the actual 3D volume data For details on the storage see the AF NI plugins manual The files in a dataset have highly structured names and these names should not be casually altered or AFNI will not be able to read them The general form of the dataset filenames is prefix view NAME where prefix is to be supplied by the user you and presumably would be used to indicate the type of data stored in the file e g spgr for Spoiled GRASS func for functional intensity etc The view code indicates the origin of the data and is assigned by AFNI the possibilities are orig for original data untransformed by AF NI acpc for datasets which have been aligned to the AC PC line tlrc for datasets which have been transformed to the Talairach Tournoux grid Datasets in the tacpc and tlrc views would normally be created by AFNI orig files would be created by to3d The NAME suffix is HEAD for the header file and is BRIK for the brick file One reason for splitting the auxiliary information from the volume data in each dataset is for efficiency
52. ls are square This can produce a blocky looking image To force a smoothing the Warp on Demand mode should be used A AFNI verbal v1 time orig amp fnew 1234 orig Sample Graphing Window 4 4 Graph Display When the current anatomical dataset is 3D time and is not set to warp on demand using the Datamode controls then the three buttons next to the buttons will be activated These allow the display of graphs of voxel intensity vs time Although AFNI MCW AFNI 2 00 19 Dec 30 1996 kkk kkk Graph scaling graph windows look very like the graph window in the auxiliary program FD2 there is at least one major difference AFNI graph windows can be resized The above figure shows a sample with 3 x 3 data time series sub graphs displayed The central sub graph is bordered in a light color here a shade of gray This sub graph is a plot of the data time series at the viewpoint voxel the one displayed at the crosshairs in the image viewing windows The other sub graphs are of neighboring pixels in this case in the sagittal plane In the corresponding sagittal viewing window the crosshairs will show a box outlining the pixels being graphed If you shift the viewpoint in an image viewer then the graph viewpoint will shift accordingly The voxel indexes of the viewpoint are shown at the lower left edge of the graph display for example Z 8 means that this is slice number 8 counting from 0 Then the spacing
53. nd gives nice results Edge Detect Sobel edge detection is performed on the image prior to display If more than one of these are selected they are performed in the top to bottom order as displayed also these operations are performed after any Tran functions 4 3 5 Control This button takes one of three forms depending on the choices made in the panel This form of the Save function is selected by toggling on the option on the control panel In this form the action is to save the current image to disk This is the only way provided by AFNI to save a montage layout This button pops up a little chooser window which asks you to input the filename prefix for the output image The image will be saved in the raw PNM format with the name prefix pnm Images in this format can be converted to other formats such as TIFF with command line utilities in the netpbm package or the xv shareware program Images which contain no color will be saved in the PGM format images with colored pixels will be saved in the PPM format MCW AFNI 2 00 15 Dec 30 1996 This form of the Save function is selected by toggling on the option on the control panel In this form the action is to save a collection of slice images underlay and color overlay to disk in the raw PNM format Even if a montage is being displayed only single slices will be saved with this function This button also pops up a chooser window which asks you to input t
54. ne MMAP_THRESHOLD to be 1 This will make AFNI use malloc and fread to access the BRIK data This will also strongly limit the number of datasets that can be used If you receive a message that AFNI cannot load a dataset into memory or mmap it then you should restart the program with the purge option This will force datasets not MCW AFNI 2 00 37 Dec 30 1996 in immediate use to be purged from memory and to be munmap ed which might solve your problem This will also make the program run slower when you switch between datasets 6 2 machdep h This C header file contains machine specific settings If you are porting AFNI to a system not available at MCW you will have to create a Makefile appropriate for your computer and will have to edit machdep h to set various flags correctly In particular flags for mmap and dynamic loading of plugins must be set correctly Comments in this file describe the options that are available 6 3 X11 Resources for AFNI Included in the MCW AFNI distribution is a file called AFNI Xdefaults This contains examples of how various features of AFNI can be controlled using X11 resources 6 4 Formula for Bk Resampling Define the cardinal basis function 1 8z 0 lt z lt 3 o z 4 81 z 5 lt 2 lt 1 0 1 lt a Then blocky interpolation in 3D of a function defined on a grid with spacings Az Ay Az to an arbitrary point in space is puns SAN ZJN _ kA f x y 2 Ld FliAn jay
55. ne will work properly if the dataset being viewed in one controller is just the realization of the other controller s dataset in a different coordinate system it will carry out the Talairach transformation or its inverse as needed to keep the lock anatomically reasonable It will fail if the two controllers have different coordinate systems and different datasets for example it doesn t know how to transform from Talairach coordinates in one dataset to Original coordinates in another dataset MCW AFNI 2 00 34 Dec 30 1996 4 8 4 Plugins The last item in the Datamode control panel is the menu button This will only be present if AFNI is compiled with plugin support and if the program finds at least one plugin when it starts up Plugins are external C functions written in conformance with the plugins manual that provide extra functionality to AFNI They are compiled into shared objects or shared libraries with the filename suffix so or s1 on HP UX AFNI searches for them in a set of directories specified in the shell environment variable AFNI_PLUGINPATH If this is not defined then PATH is used that way storing the compiled plugins in the same place as the MCW AFNI executables will work Each plugin will create one or more interface panels When you select a plugin from the menu its interface panel will pop up At that point you fill in the desired parameters and then execute the actual plugin code with
56. nterpolate vs 8 for Li and Bk and it uses more complex formulas this is understandable For most purposes Li interpolation for anatomical images and Bk interpo lation for functional images will be the best N B threshold data in functional datasets is always resampled using the NN mode This is because it is somewhat unreasonable to interpolate a nonlinear statistic such as correlation coefficient between voxels and then to interpret this statistic using probabilistic models that assume independence The smallest resolution allowed by the Resam mm selector is 0 1 mm This is very tiny and images will display very slowly You can do it if you wish however don t try to write out a whole human head dataset to disk at this resolution The disk space required would be rather large Controls for determining whether the functional dataset BRIK if available or warp on demand will be used for computing the functional slices are the next set down The functional BRIK can be used only if it actually exists in the current view i e coordinate system and if it is at the same spatial resolution as the anatomical dataset being viewed 4 8 2 Dataset Output and Input The Write buttons will compute and write the BRIK files to disk for the indicated datasets The current resampling mode and resampling dimension will be used for this purpose The button will output the current anatomical dataset the button outputs the current functional data
57. of access to the brick file Another reason is that in an emergency the auxiliary information is stored in ASCII form and so can be edited manually this requires extreme care A third reason is that when transformed datasets tacpc and tlrc are created their brick files may be deleted later to save disk space as long as the transformed header files and the torig brick files exist AFNI can recreate the transformed data Once raw images have been put into the AFNI dataset format they are no longer needed for any of the programs described herein It is always possible using AFNI or from3d to extract images out of the 3D data brick although you may then have to convert them into whatever format you desire If you choose to rename the pair of files that make up a dataset the only part you should touch is the prefix If you alter the view or NAME parts AFNI will probably refuse to read the files at all Not all datasets will have a BRIK file AFNI is capable of transforming data from a parent dataset as needed for image display If the necessary transformation e g from orig to tlrc is available then the child dataset e g the tlrc dataset need not have a BRIK file it can be warped on demand for display Normally torig datasets do not have a warp parent dataset so they must have a BRIK file An exception to this rule can be created with the auxiliary program 3ddup At this time no program but AFNI itse
58. ood and Drug Administration for any clinical application Ownership and License to Use This software and its associated manuals are Copyright 1994 96 by the Medical College of Wisconsin Permission is granted to make use of and to make copies of this software and its manuals for non commercial research purposes only Use of the software or its manuals by for profit organizations is prohibited without prior written permission Redistribution of this work or any derived work outside of the licensed organization is prohibited without prior written permission Copies may be made within the licensed organization without separate permission from the Medical College of Wisconsin Distribution and Registration MCW AFNI is available free for research purposes but users must register with the Medical College of Wisconsin For information send an e mail re quest to the author at rwcox mcw edu write to the address above or see the final page of this manual Acknowledgement This work was developed with internal MCW funds and was also partly supported by the United States NIH through grants MH51358 and NS34798 Contents 1 Introduction 3 4 7 Define Function 31 4 7 1 Threshold Slider 31 2 What s New 4 4 7 2 Color Pbar 32 4 7 3 Options 32 3 Fundamentals 6 4 3 Define Datamodel 33 3 1 Datasets a ee er ee ee ee 6 4 8 1 Resampling 33 3 2 WOSSIONS a 2 Abate gS khan ele 9 4 8 2 Dataset Output and In PU ed Bek
59. r constituent anatomical and functional datasets It is important to understand the dataset concepts file structure and directory hierarchy described and depicted above Sessions are referred to by the top level directory name under which all their datasets reside An individual dataset is referred to on auxiliary program command lines by the name of its header file the name of its brick file or just by the prefix view part of the filenames for example 12dec94 func03 acpc HEAD 12dec94 funcO3t acpc BRIK 12dec94 funcO03 acpc would all refer to the same dataset residing in a given session directory By moving to the directory above the session directory you can save and compress all the files in a session using the command tar cvf session_directory gzip 9v gt session tgz This presumes that you have the GNU gzip compression utility installed on your system The command to uncompress and restore from the compressed archive would be gzip dc session tgz tar xvf MCW AFNI 2 00 9 Dec 30 1996 4 A Tour of AFNI The best way to learn the program is to read this tour through and then sit down with the program and try it out 4 1 Starting Up The command line to run AFNI is quite simple afni sessionil session2 Here session is the name of a session directory to read in All the 3D datasets under each named session directory will be read in If no sessions are specified on the command line the current working directory wil
60. ral unlabeled button causes the crosshair gap to close clicking this button again causes the gap to open up again This is very useful when positioning the crosshairs prior to setting an anatomical marker Ps No Rotation CCH 90 Rot 180 CH 90 O LR Mirror m No Overlay a 2 to 98 oO Free Aspect Nsize Save lt PNM Save Montage Controls Save One i Across T op ran none Bow 1 5 Tran 20 none FI Spacing 10 EF latten Border of O Sharpen O Edge Detect Color none Reset Done Quit 1x1 Draw Set Image viewer and control panels 4 3 4 Control This button opens up a control panel pictured above that lets you change how the images will be displayed in this window The and items control the orientation of the image in the window The item allows you to turn off all color overlay items i e crosshairs anatomical markers and function The and MCW AFNI 2 00 14 Dec 30 1996 KKK netpbm and xv items choose how the values in the image array are mapped to grayscale levels on the screen The former choice maps the minimum image value to black and the maximum to white the latter choice computes the cumulative histogram of the image and maps the 2 point to black and the 98 point to white The control lets you resize the image window to any bizarre aspect ratio Normally the program restricts the image window resizing
61. rposes by clicking Button 1 on the logo Clicking Button 1 in that space again will restore the logo The and buttons will also be hidden and restored by these operations Clicking Button 1 on the central sub graph will cause the time index to jump to that point If the Shift or Ctrl key is pressed while doing this the time index instead will move up or down by 1 in whichever direction corresponds to the mouse cursor relative to the time index indicator ball Clicking Button 1 on any other sub graph will cause the spatial viewpoint to jump to that location without changing the time index Clicking Button 3 on a sub graph will popup a small window with some statistics about that time series Some keystrokes if pressed while the graph window has focus will carry out certain functions These functions are also available from the menu and are described below MCW AFNI 2 00 20 Dec 30 1996 Cancel Pick Ideal Pick Ort Edit Ideal i Ideal Center mi Smooth Ideal Shift Ideal Clear Ideal Clear Ort Read Ideal Write Ideal Store Ideal Ignore FIM Plots Refresh Freq Compute FIM Grid M a Ideal Center Cancel TDown Matrix Ae Choose Slice Grid Color r Baseline b Hrite Center Cw Set w Suffix Tran OD none af Tran 1D none al I Double Plot Graphing left and right menus 4 4 2 menu The items on this menu control
62. s of datasets are treated identically The only reason for choosing a particular anatomical type is to remind yourself of the dataset s origin Anatomical datasets may be in the 3D or the 3D time format The 3D format stores one value per voxel The 3D time format stores a series of values per voxel This can be used to stored all the data from a 3D FMRI imaging run The auxiliary program 3dfim or the internal AFNI FIM capability can be used to produce functional activation datasets from 3D time datasets Within the class of functional datasets there are presently five types fim Functional Intensity e one value is stored per voxel MCW AFNI 2 00 6 Dec 30 1996 KREK n Atomic datum fith Functional Intensity Threshold e two values are stored per voxel e the first is intensity defined arbitrarily e the second is threshold which is a either a floating point num ber between 1 0 and 1 0 or a 2 byte integer between 10000 and 10000 which can be used to select which voxels are consid ered active fico Functional Intensity Correlation e two values are stored per voxel e the first is intensity e the second is a correlation coefficient between 1 0 and 1 0 which can be used to select active voxels at a given significance p value fitt Functional Intensity t test e two values are stored per voxel e the first is intensity e the second is a t statistic which can b
63. s been extended down inferior by 10 mm This is to make sure that the brick includes the entire cerebellum which is not the case using the old brick dimensions taken from the Atlas 9 Threshold Resampling The type of interpolation used for functional dataset resampling is controlled by the button in the Datamode control panel In AFNI 1 0x both the functional intensity fim and the threshold data were resampled using the chosen method In this version of AF NI the threshold data e g correlation coefficient is always resampled using the NN method This is because thresholding with an interpolated nonlinear statistic is a somewhat dubious procedure 10 Multiple AFNI Controllers Using the button you can open up multiple controller windows in a single run of AFNI This allows you to view more than one dataset at a time Using the menu you can force the coordinates of the different viewing windows to be locked together This feature allows you to scroll in unison through multiple datasets MCW AFNI 2 00 D Dec 30 1996 KkK e gt Crucial information KKK 3D time 11 Session Directories If you don t specify any directories on the command line then AFNI acts as if you had typed that is it will try to read datasets from the current directory The new R switch will tell AFNI to read from all subdirectories of the given session directories recursively Using the Rescan buttons you can re read se
64. set The button allows you to select more than one dataset from all sessions and write them all out This new control is provided since the resampling process can be relatively slow now you can select many datasets start their output in Talairach coordinates and then go get something good to eat while AFNI churns away MCW AFNT 2 00 33 Dec 30 1996 kkk kkk Try this AFNI will not write over a dataset BRIK which cannot be recreated by warping from a parent This precaution does not extend to plugins which can be written so as to destroy unrecoverable BRIKs It is possible to use AF NI to resample a dataset in the orig view but only if the dataset is warp on demand from another dataset as parent This can be arranged using the 3ddup auxiliary program The Rescan buttons are designed to re read data from disk The first one This will re read the current session This is useful if you use an auxiliary program such as 3dANOVA to create a new dataset outside of AFNI and then wish to view it In earlier versions it was necessary to exit AFNI and restart it to get new datasets into the program The button will re read all the sessions that were initially loaded there is no facility to read in an entire new session at this time Finally the button will re read the time series directories and load any new time series files that are found 4 8 3 Controller Lock With the button lower left of AFNI controller window
65. set moving within a slice is controlled by Button 1 clicks as described above Grid Color This item just rotates the vertical grid color between the available choices MCW AFNI 2 00 21 Dec 30 1996 This item switches the way that graph baselines are computed By default each sub graph has the minimum value of its time series mapped to the bottom of its sub window By pressing this item or the b key the sub graphs will switch to having a common baseline That is the minimum value in all the displayed time series will mapped to the bottom of each sub window In many cases doing this will require scaling down the graphs with the key Choosing this item again will restore the original graph baseline mode Selecting this item or pressing the w key will write the dataset time series in the central sub graph to disk in a filename like 033_034_008 suffix 1D The suffix is selected by the next menu item Set w Suffix and the prefix numbers are from the voxel spatial index in the dataset The output file is ASCII one number per line N B the output is the dataset time series and is unaffected by the Tran transformations below Tran OD This item is the same as the item on the image viewer panel It allows the application of a pointwise transformation function to the time series before graphing occurs This item allows the application of general transformations to the time series before graphing
66. so as to keep the data voxel to display pixel geometric relationship correct assuming that display pixels are square The controls actually have nothing to do with image display They are just here because it was a convenient place to put them They control the operation of the button on the image viewing window next to the button this is discussed below The Tran menus allow you to pick from a list of image transformations The transformations are all pointwise that is the image intensity output at a given pixel is a function of the image intensity input at that given pixel only The built in functions are and SSqrt which take the common logarithm log of each pixel and take the signed square root sgn x z of each pixel respectively functions are more global image transformations where the image intensity output at a given pixel can be a function of other pixels The only built in function is Median9 which replaces each pixel by the median overs its 3 x 3 neighborhood AFNI plugin authors can add functions to these Tran menus hopefully they will be doc umented At the bottom of the panel are 3 other built in image processing functions Histogram flattening or equalization is performed on the image prior to display High emphasis sharpening is performed on the image prior to display When printing images on printers with relatively few colors available per pixel the combina tion of a
67. ssions This is useful if you use an auxiliary program e g 3dmerge to create a dataset and then want to import it into AFNI 12 Writing Many Datasets to Disk at Once A new button allows you to select many datasets at once for output to disk This makes it possible to start a long Talairach output session and then leave the computer unattended while it computes each output BRIK 3 Fundamentals This section explains how data is organized in the MCW AFNI package The two indis pensable concepts are datasets and sessions 3 1 Datasets The fundamental unit of data in AFNI is the dataset one or more 3D bricks of imaging data together with some auxiliary information e g axes orientation coordinates of marked fiducial points There are two classes of datasets anatomical and functional An example of the former would be a Spoiled GRASS MRI scan An example of the latter would be the results of cross correlating a functional MRI FMRI time course of images 2 When you create a dataset using the to3d program you must specify whether it is anatomical or functional in nature When you are using AFNI at any given time you will be displaying one anatomical dataset as the grayscale underlay and possibly one functional dataset as the false color overlay Within the class of anatomical datasets to3d provides you with a list of possible types e g Spoiled GRASS Echo Planar MR Angiogram At present all anatomical type
68. t is generating a new ID code These ID codes are pseudorandomly generated using the current time and machine name as seeds For more information see the plugins manual If you use the Unix command cp to copy a dataset then the new dataset will have the same ID code as the original AFNI will not run correctly if two such datasets are read into the program To fix this you can use the auxiliary program 3dnewid to attach a new ID code to a dataset 5 3D time Datasets AFNI now supports time dependent 3D datasets which I refer to as 3D time datasets At present only anatomical datasets may be usefully set up to be time dependent 3D time datasets are created with to3d using the new time zt or time tz com mand line switches 3D time datasets can be viewed in the image viewing windows in the usual orthogonal slices Scrolling in time through these views is a good way to check for subject movement They can also be graphed vs time similar to the program FD2 6 Interactive Functional Activation Analysis AFNI now has the ability to run the equivalent of the fim2 program on a 3D time dataset producing as output a new 3D fico dataset 7 Image Montage One of the most visible changes to AF NI itself is the addition of the montage display of an array of slices feature to the image viewing windows This is accessed using the new button 8 Big Talairach Box The size of the default Talairach coordinates brick ha
69. tlrc HEAD ln s GRP tlrce HEAD fred GRP tlrc HEAD ln s GRP tlrc BRIK fred GRP tlrc BRIK ln s GRP tlrc HEAD ethel GRP tlrc HEAD ln s GRP tlrc BRIK ethel GRP tlrc BRIK In s GRP tlrc HEAD lucy GRP tl1rc HEAD In s GRP tlrc BRIK lucy GRP tlrc BRIK The ln s commands put links to the GRP anatomy dataset into each of the session directories In this way if the user runs AFNI with the command afni fred ethel lucy then each of the sessions will have access to the GRP dataset but there will only be one physical copy of it on disk A problem arises with this scheme because of the manner in which AFNI accesses large brick files The program will not recognize that the links point to the same actual file and it will attempt to mmap the GRP tlrc BRIK file more than once This will likely fail and the program will crash when the second access is attempted when the user switches to the second session Using the purge switch will avoid this problem Before a new dataset is accessed when switching sessions anatomies or functions existing dataset bricks will be be munmap ed This will prevent the attempt to mmap the same brick file twice at the same instant Another way to approach this problem would be through the use of the 3ddup pro gram to create warp on demand copies of the GRP tlrc dataset in each of the session directories e R Recursively searches each session_directory for more session subdirectories This will descend the ent

MCW ¤¥¦¨ User Manual Medical College of Wisconsin

Contents

Download Pdf Manuals

Related Search

Related Contents

MCW &curren;&yen;&brvbar;&uml; User Manual Medical College of Wisconsin

Contents

Download Pdf Manuals

Related Search

Related Contents

MCW ¤¥¦¨ User Manual Medical College of Wisconsin