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BrainNet Viewer Manual (PDF version, 1M)

1. The option panel has three parts Fig 10 The list box on the left includes Layout Background Surface Node Edge Volume and Image which represent different aspects of the figure The main panel on the right shows the detailed options of each part click the text in the list box to change the panel There are six buttons on the bottom of the panel use the Load and Save options to acquire or save a mat file Reset to return all parameters to their original state OK or Apply to draw graph and Cancel to exit the panel without changes Bl option o amp s r Layout Background Surface Single view Node Edge Volume Image View direction Sagittal Axial Coronal Full view Load Save Reset OK Apply Cancel Fig 10 Option panel 5 1 Layout panel This panel is used to set the output view of the brain model The Single view option shows only one brain model and can be set as Sagittal Axial or Coronal view while the Full view option provides six or eight depending on whether the brain surface can be divided into left and right hemispheres brain models See Fig 10 and Fig 11 11 BrainNet Viewer User Manual 1 0 July 11 2011 Single view Full view Fig 11 Different layouts 5 2 Background panel To change the color of the background
2. Contents k dntroductloliseeentecneeeem b mena ate E ERU MM LU 2 MEN rere Rm 3 2 1 Run BrainNet Viewer on a PC with Matlab eeeeerern 3 2 2 Run BrainNet Viewer on a PC without Matlab cc ceecccsssccceseeeeeseeeeeeeeeees 3 EN a e E a E S tases S ES S 4 A OAF a e E E E 5 AL oda SU ACO la E EA E es 5 Ar Eoo VOCS Re TRO 7 43 WO AAI COS TB inserire UO HaT d Pa M IC PII PM NEIN AERE AS 8 aA lodda voume TE ccesesundisibehmti icivie T foisiet quercus aiss m esL EOD 9 SR WISU AI OPO MEET umT 11 SENE OUI I MT Em 11 o7 BackBround D3ITOLossesseedvtiuisast imer abri E dubbiMi uU eae 12 M MEE V gcio Se INE TET 12 2 EE eode m 13 v HE ordo METTUS n 15 SN MER iu deam 17 D NAVAS Dale acuesiesemmt deca N E N E A I CRI TEUEUU 18 EU uv nH 20 ME e OM 20 MEME See E Em 21 32 8 2 0 eee ene ee A eee ee eee 21 s E oro emm 21 sf lom 22 F WOON DA E E ETE E E E 23 7 JoadTies S save ds WAS eC nuenian TEE 23 Pe PANETE ZOO Ms RT E E TE 23 7 3 Move Rotate amp Get POSITION sssssessessesssrssessersrrssessessersresseoserseesseeseesreesees 24 74 Standard VEW a E E A E T NU MUERE 24 Ba DOMO a a A E T E 25 PIO OC OTN N p EASE EA EE EEA 26 1 BrainNet Viewer User Manual 1 0 July 11 2011 1 Introduction BrainNet Viewer is a brain network visualization t
3. re render the brain model depending on the current orientation Click the Get position button and then click on the surface of the brain to show the coordinate of the vertex Right click anywhere in the figure window and select Delete All Datatips to remove all coordinate labels 7 4 Standard view Three standard views sagittal axial and coronal view buttons are available to help users observe networks from different standard views quickly These buttons should only be used for Single view visualized brain networks Click twice to see the opposite side of the brain 24 BrainNet Viewer User Manual 1 0 July 11 2011 Sagittal View Axial View Coronal View Fig 23 Standard views 7 5 Demo Press the black triangle button to make the brain rotate clockwise until the black square button is pressed This function only works for Single View visualizations 25 BrainNet Viewer User Manual 1 0 July 11 2011 Acknowledgements We thank the following colleagues for their kind helps during BrainNet Viewer developing and manual revising Dr Gaolang Gong Dr Ni Shu Mr Jinhui Wang Mr Teng Xie Mr Qixiang Lin Ms Zhengjia Dai Ms Miao Cao and Ms Jiaying Zhang National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University China Professor Alan Evans McGill University Canada Mr Patrick Clark Pennsylvania State University USA We also thank the developers of the following softwares an
4. 16 56 47 32 13 31 4 0 00 E 18 49 48 1 14 02 4 0 83 ORBsup R 33 43 32 73 35 46 3 2 27 MFG L 37 59 33 06 34 04 3 2 427 MFG R 30 65 50 43 9 62 3 0 55 ORBmid L 33 18 52 59 10 73 3 0 57 ORBmid R 48 43 12 73 19 02 3 1 98 IFGOperc L 50 2 14 98 21 41 3 0 03 IFGOperc R 45 58 29 91 13 99 3 0 53 IFGtriang L 50 33 30 16 14 17 3 0 47 IFGtriang R 35 98 30 71 12 11 3 0 17 ORBinf L 41 22 32 23 11 91 3 0 03 ORBinf R 47 16 8 48 13 95 1 2 00 ROL L 52 65 6 25 14 63 1 0 27 ROL R 5 32 4 85 61 38 3 0 92 SMA L 8 62 0 17 61 85 1 0 00 SMA R 8 06 15 05 11 46 5 0 49 OLF L 10 43 15 91 11 26 4 0 23 OLF R 4 8 49 17 30 89 4 3 30 SFGmed L 9 1 50 84 30 22 4 0 59 SFGmed R 5 17 54 06 7 4 4 1 20 ORBsupmed L Fig 6 Node file AAL90 4 3 Load an edge file The brain edge file is defined as an ASCII text file with suffix edge representing a connectivity e g correlations matrix among the ROIs which could be weighted or binarized and therefore the dimensions of the matrix must correspond to the number of nodes AAL90 Brodmann82 HOA112 Dos160 160 ROIs from Dosenbach et al Science 2010 and other e g customized ROIs by users files are provided and each file is in the folder Data ExampleFiles corresponding to its template name You can generate your edge file according to the requirements BrainNet Viewer User Manual 1 0 July 11 2011 i T BP Load File so J amp J 93 j Load File
5. Draw nodes This function is used to decide which nodes are to be drawn Select Draw All to draw all nodes in the file or set a threshold of color or size corresponding to column 4 or column 5 to draw those nodes with higher value than the threshold Nodal label This panel is used to control the nodal label Three options are available Label All Label None or by a threshold that only label those nodes with higher value than the threshold on size or color Click the Font button to change the font of the labels in the popup dialog Nodal size There are two ways to set the size of the nodes First use the value in column 5 in the node file In this manner you can choose Auto to arrange the sizes of nodes to a proper range radius 2 7 by their value automatically or choose Raw to use the original value in column 5 in the node file When a threshold is selected the nodes below the threshold will be a small size radius 1 while those above threshold will display by their Auto Raw size Drag the slider bar or enter the threshold in the edit box The range must be the same as that in column 5 in the node file Second set all nodes to an equal size ignoring the size value in the file and the size can be defined in the edit box The volume ratio option is used to adjust the size of all nodes together and the scale factor ranges from 0 1 to 10 Nodal color This panel provides four ways to control no
6. BrainNet Viewer User Manual 1 0 July 11 2011 22 7 Toolbar The toolbar Fig 21 provides frequently used and interaction commands to operate the brain network graph most of them are not included in the menu TELESERIAL Fig 21 Toolbar 7 1 Load Files amp Save as Image These two commands are included in menu see details in section Load Files and section Menu File Save Images 7 2 Print amp Zoom The Print command lets users print the current graph conveniently A print panel like the one below will pop up after the Print button is clicked The Zoom in and Zoom out buttons help users to focus on the local or observe the global status of brain network 23 BrainNet Viewer User Manual 1 0 July 11 2011 n Print Prenew 5 D ti StyleSheet modified Cove As Zoom Overview hf Pnnt Refeesh Heip Close Layout imes Tex Color Advanced AT eee LE Adi aane oe Format Ad 12 Nidtx 14 Hoght i 16 Unite Orientatio 18 g Inches Portra e a E IPSA entimet Landscap aL f e 4 Points Rotated 40 2 EA i ut Print panel Zoom in amp Zoom out Fig 22 Print panel and Zoom function 7 3 Move Rotate amp Get position Click the Move button and drag the brain anywhere in the window When the Rotate button is pressed hold left button of the mouse and move mouse to rotate the brain When rotate button is deselected the light cam in the window will
7. Fig 2 Brain network pictures with the BrainNet viewer BrainNet Viewer User Manual 1 0 July 11 2011 4 Load Files To draw a brain network graph some kinds of files such as brain surface node file or edge file should be loaded in the first step Click Load File button on the toolbar or File Load File in the menu to open Load File dialog shown below Fig 3 Select files to draw required graph In BrainNet Viewer we provided several brain surface templates and example files which were made from various brain parcellation methods They include 1 ICBM152 whole brain surface Colin brain surface and ICBM152 left and right hemispheric surfaces in the folder Data Surffemplate and 2 node and edge files of AAL90 Brodmann82 HOA112 Dos160 160 ROIs from Dosenbach et al Science 2010 and others e g customized ROIs by users in the folder Data ExampleFiles BBP Load File o amp s Load Files Surface file Browse Data file node Browse Data file edge Browse Volume file Browse Reset OK Cancel Fig 3 Load File dialog 4 1 Load a surface file Click the Browse button next to the Surface file in the Load File dialog and then select the required brain surface file in the popup dialog BrainNet Viewer provides two different brain templates ICBM152 Data SurfTemplate BrainMesh_ICBM152 n
8. color by a given threshold drag the slider bar or enter the 16 BrainNet Viewer User Manual 1 0 July 11 2011 threshold into the edit box The range must be the same as the correlation matrix in the edge file Right click the color square to select colors the left one represents the higher value while the right one represents the lower value Fourth binarize the color by a given threshold of Euclidean distance between two nodes mm The edges with longer length have one fixed color while the shorter ones have another fixed color Drag the slider bar or enter the threshold in the edit box the threshold can range from zero to 100 Right click the color square to select colors the left one represents the higher value while the right one represents the lower value 5 6 Volume panel This panel is used to control the mapping of the volume file NIFTI and analyze paired images to the brain surface The volume file could be a T map Z map an atlas image etc F E Option ol m fs Layout Volume Mapping Background Surface Volume Data Range 4 72 3 75 Node Edge Volume Display Positive amp Negative v Image Positive Range 0 01 3 Negative Range 0 01 3 Color for Null E Colormap Jet X Load Save Reset OK Cancel Fig 16 Volume panel The Volume Data Range shows the minimum and maximum values of the volume file The Display option contains three mapping possibi
9. to change the threshold when a weighted matrix is loaded or it will draw the full connection among the nodes which would require a lot of time Edge size There are two ways to set the size of edges here size means the radius of the edge First employ the correlation matrix value in the edge file In this manner you can choose Auto to assign the edge sizes a proper range radius 0 3 1 5 by their value automatically or choose Raw to use the original value of the correlation matrix in the edge file When a threshold is selected the edges with values lower than the threshold will have a fixed smaller size while the edges above threshold will be shown as Auto Raw size Drag the slider bar or enter the threshold into the edit box but the range must be the same as the correlation matrix in the edge file Second set all edges to an equal size and the size can be defined in the edit box The scale option is used to adjust the size of all edges together The scale factor ranges from 0 1 to 10 Edge color This panel provides four ways to control edge color First to adopt the same color for all edges right click the color square and select the required color from the popup dialog Second use a colormap to render the value of the edge from low to high corresponding to the values of the correlation matrix in the edge file 13 kinds of colormaps same as the nodal colormaps can be selected Third in order to binarize the
10. The size output Image is set here Image width and height in pixel dimension or in document size both cm and inch and dpi of the graph can be defined here Fig 18 18 BrainNet Viewer User Manual 1 0 July 11 2011 o v Fig 18 Image panel BrainNet Viewer User Manual 1 0 July 11 2011 19 6 Menu 6 1 Files Load files Click to open load files panel for more details see Section Load Files Save Image g m Success fo eo ls After visualization click here to save the present figure as an image At present TIFF BMP EPS JPEG and PNG image formats ali are supported The parameters of the image such as pixel dimension document size and dpi can be adjusted in the Option panel lmage After the image is saved a message box appears see right picture Save Movie This function helps users to save a demonstration movie for network visualization It produces a 12 seconds long 30 FPS 735 X 534 avi file in which the brain network rotates clockwise in a circle one degree per frame This operation will take about 10 minutes Please drink a cup of coffee to wait before playing the movie Note that this function should only be used in the Single view layout Pictures below show different frames at different times For an example see http www nitrc org docman view php 504 1023 Demo 20V ideo96200f9620Brain9620N etwork 20 14M Fig 19 Frames of the network movie E
11. d toolboxes whose source codes or file formats were referenced during our package developing Matlab http www mathworks com products matlab SurfStat http www math mcgill ca keith surfstat FreeSurfer http surfer nmr mgh harvard edu BrainVISA http brainvisa info 26 BrainNet Viewer User Manual 1 0 July 11 2011
12. dal color First to use the same color for all nodes ignoring the color index in the file right click the color square and select the required color from the popup dialog ok 5 Second use a color map to display the value of the nodes from low end to high end corresponding to column 4 in the node file 13 kinds of color lt Lu HE 2 2 EM a 7T maps can be selected see the right picture for detail sks 5 gt CD lt cerwo amp Third modular color can be used to display different nodal colors for different modules 14 BrainNet Viewer User Manual 1 0 July 11 2011 Buses Set the values of column 4 as 1 2 3 corresponding to modular 1 was 7 B modular 2 in the node file The maximum number of modules is21 at present Click to open the modular color dialog and the left uodas AE picture will display six modules with their color on the right Click the Modules MI popup menus on the left to select other modules in the list and the woe ag color square will change to the corresponding one Right click the wo em color square to change color as described above Fourth to binarize the color by a given threshold drag the slider bar or enter the threshold in the edit box but the range must be the same as the range stated in column 4 of the node file The nodes with higher value will have one fixed color while the nodes with lower value will have anot
13. du and the Colin27 brain surface was made by BrainVISA http brainvisa info We transferred and merged the original bilateral hemisphere files into one nv file A surface merge tool is in details in section Menus Tool the tools menu see more Currently the pial files generated by FreeSurfer only hemisphere mesh and the BrainNet Viewer User Manual 1 0 July 11 2011 mesh files generated by BrainVISA are supported and these can be loaded and visualized directly The FreeSurfer pial files are recommended as their vertex coordinates have been transformed into the MNI space while the BrainVISA mesh files may need a manual transformation The ICBM152Left nv and ICBM152Right nv files are from Professor Alan Evans s group in the Montreal Neurological Institute McGill University Of note the coordinates in the surfaces are located in the MNI space 4 2 Load a node file The file represents the information from ROIs obtained from the AAL90 Brodmann82 HOA112 Dos160 160 ROIs from Dosenbach et al Science 2010 and others e g customized ROIs by users Each file is in the folder Data ExampleFiles corresponding to its template name Click the Browse button next to Data file node in the Load File dialog and select the required node file The AAL90 node file is selected in Fig 5 BB Load File al e s r Load Files Surfac
14. e file Browse Data file node Data file edge Browse Volume file Browse Reset OK Cancel m aJ Select File to Open Lookin AAL90 ef rt E3 s Name p Date modified Type ti epee eee eee een e eser eire Yee YHP YET CEES CEES YEEYYEEEYYPF EEEE EEEE PYY EERE PVP EEE EER EERE H Fi Rec Places ok Node AALSO node rc 2011 5 31 11 06 NODE File Desktop i E i Libraries Computer Network 4 m p File name Node_AAL90 node v Files of type Node files node Y Cancel Fig 5 Select node file AAL90 is selected BrainNet Viewer User Manual 1 0 July 11 2011 The node file is defined as an ASCII text file with the suffix node In the node file there are 6 columns column 1 3 represent node coordinates column 4 represents node colors column 5 represents node sizes and the last column represents node labels Please note a symbol no in column 6 means no labels The user may put the modular information of the nodes into column 4 like 1 2 3 or other information to be shown by color Column 5 could be set as nodal degree centrality T value etc to emphasize nodal differences by size You can generate your nodal file according to the requirements r Node AAL90 node Notepad File Edit Format View Help 38 65 5 68 50 94 4 4 96 a 41 37 8 21 52 09 4 0 86 PreCG R 18 45 34 81 42 2 4 1 99 21 9 31 12 43 82 4 2 40 SFGdor R
15. her fixed color Right click the color square to select the color the left one represents the higher value color while the right one represents the lower value color 5 5 Edge panel There are three parts in this panel to control edge drawing edge size and edge color separately nm H Option fol m fs Layout E Edge Background Draw Edge Surface Node Draw All Edge Volume Image Above Threshold 4 b 0 54 Sparsity af gt 0 05 V Absolute value Size Value Auto v Equal 0 30 Threshold 0 00 7 Absolute value Scale b 1 00 x Range 0 1 10 Color Same Bi Colormap Hot v Absolute value Threshold do gt 0 00 mm Em ewm lt oo NP Fig 15 Edge panel 15 BrainNet Viewer User Manual 1 0 July 11 2011 Draw Edge This panel is used to extract edge information from the correlation matrix contained in the edge file and to decide whether all or parts of them are to be drawn Select Draw All to extract and draw all edges all values not equal to zero in the correlation matrix select Threshold to extract the edge above a threshold This threshold can be set as a value in the matrix or in the sparsity of the matrix Check Absolute value to extract the absolute value of the matrix Note that BrainNet Viewer will treat the value zero 0 in the matrix as a null edge and only the right upper triangle of the matrix will be considered Always remember
16. lities Positive amp Negative Positive only and Negative only Positive amp Negative sets the colorbar range from the minimum negative value to the maximum positive value and Positive only and Negative only just set the range of the colorbar in positive value or negative value 17 BrainNet Viewer User Manual 1 0 July 11 2011 separately Positive Range and Negative Range are used to set the range of the color bar The edit boxes on the left define the value near zero on the color bar while the right ones define the value away from zero Take the above picture as an example When Positive amp Negative is chosen the color bar would be arranged from 3 to 3 and 0 01 to 0 01 would be set as the null value range if Positive only is selected the color bar would be arranged from 0 01 to 3 any value below 0 01 would be set as a null value and if Negative only is selected the color bar would be arranged from 0 01 to 3 and any value above 0 01 would be set as a null value see Fig 17 f q 1 45 1 15 Positive amp Negative Positive only Negative only Colormap Jet Colormap Hot Colormap Winter Fig 17 Volume mapping Color for Null defines the color for null value part on the surface Right click the color square and select required color Colormap provides 13 kinds of color maps same as the colormap available in node and edge color 5 7 Image panel
17. lly running the BrainNet viewer r BrainNet Viewer j mm File Option Visualize Tools Help Gu s uuoowdecgc ob btS BrainNet Viewer Version 1 0 RC 1 A flexible and rapid network mapping tool b National Key Laboratory of Cognitive Neuroscience and Learning 2 Beijing Normal University Contact Infomation Mingrui Xia mingruixia o gmail com Yong He yong h he gmail com Fig 1 The Interface of BrainNet Viewer BrainNet Viewer User Manual 1 0 July 11 2011 3 Pictures BrainNet Viewer will not load surface node edge and volume file together The following combinations are acceptable and different combinations will generate different network pictures see Fig 2 1 2 3 4 5 6 Brain surface load brain surface file only See section 4 1 Nodes load node file only See section 4 2 Brain surface and nodes load both brain surface and node files See sections 4 1 and 4 2 Nodes and edges load both node and edge files See sections 4 2 and 4 3 Brain surface nodes and edges load brain surface node and edge files together See sections 4 1 4 2 and 4 3 Volume mapping to surface load brain surface and volume files See section 4 1 and 4 4 Tae TN se 9 6 oF Tae ui PROPUFT ad P ws amp ee c eI fg o 9 e e a M TIT e Re 3 e c pT cet 5 Surface Nodes amp l 4 Nodes amp Edges e 6 Surface mapping ges
18. ool which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick easy and flexible way It would be greatly appreciated if you have any suggestions about the package or manual Developed by Mingrui Xia National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University China Contact information Mingrui Xia mingruixia gmail com Yong He yong h heQ gmail com yong he bnu edu cn Please cite as was were visualized with the BrainNet Viewer http www nitrc org projects bnv while using the package to make publicized pictures Copyright 2011 Dr Yong He s Lab National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing China BrainNet Viewer User Manual 1 0 July 11 2011 2 Installation 2 1 Run BrainNet Viewer on a PC with Matlab Run Matlab Add BrainNet Viewer path to Matlab search path Type Addpath x BrainNet where X BrainNet means the path of BrainNet Viewer on the machine Run BrainNet m Type BrainNet 2 2 Run BrainNet Viewer on a PC without Matlab Install Matlab Components Runtime MCRInstall exe version 7 14 170MB using default settings contact us if you do not have Restart your computer strongly recommended Run BrainNet exe it should take about one minute to start You can find the interface below Fig 1 after successfu
19. or node and edge files in the load file dialog should be left blank The principle of volume mapping is to transfer the vertex coordinates on the brain surface to the nearest volume in the image file and assign vertices to corresponding values Bl Lod File e amp 5 Load Files Surface file Browse Data file node Browse Data file edge Browse Volume file ee mda nac r Select File to Open 4 File name Files of type Name i Pos AD NC ROIO1 T hdr Pos AD NC ROIO1 T im Pos AD NC_ROI02_T hdr 4 Pos AD NC_ROI02_T img Pos AD NC ROI03 T hdr 4 Pos AD NC ROIO3 T img Pos AD NC_ROI04_T hdr 4 Pos_AD NC_ROI04_T img Pos AD NC ROIO05 T hdr 4 Pos AD NC ROI05 T img Pos AD NC ROI06 T hdr 4 Pos AD NC ROIO6 T img Pos AD NC ROIO7 T hdr m Pos AD NC ROIO1 Timg M All Files M lookin Res UU e KB Date modified 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 2011 5 6 14 37 Type HDR Fi HDR Fi IMG Fi HDR Fi IMG Fi HDR Fi IMG Fi HDR Fi IMG Fi HDR Fi IMG Fi HDR Fi 7 h EEE Fig 9 Volume file a T test Map file is selected BrainNet Viewer User Manual 1 0 July 11 2011 10 5 Visualize option
20. please right click on the color square right beside the text color and select the desired color on the popup dialog Fig 12 Fig 12 Background panel 5 3 Surface panel This panel is used to control the color and transparency of the brain surface Please right click the color square to change color of the brain surface and drag the slider bar 12 BrainNet Viewer User Manual 1 0 July 11 2011 or enter a number range from 0 1 in the edit box to change the transparency of the brain surface Layout Surface Background Surface Color Node Ta Transparency i gt 0 20 Image Fig 13 Surface panel 5 4 Node panel There are four zones in this panel to control node drawing label setting nodal size and nodal color separately F p q M qa BB Option eJ m es Layout a Node Background Draw Nodes Surface Node Draw All Edge Volume Image Above Threshold 2 00 Size Label Label All Label None Font Above Threshold 2 00 Size Size Value Auto v Equal 3 00 E Threshold 2 00 Scale 0 70 x Range 0 1 10 Color Same E Colormap Jet 7 Modular More Threshold 1 00 B Fig 14 Node panel BrainNet Viewer User Manual 1 0 July 11 2011
21. s Surface file Browse Data file node mre p Data file edge Volume file Browse milium msi miii E Select File to Open lookin AAO s e amp rekEM s Name Date modified Type f Edge AAL90 Binary edge 2011 4 14 14 25 EDGE File Recent Places amp Edge AAL90 Weighted edge 2011 4 14 14 23 EDGE File Desktop I I Libraries A Computer ia Network 4 n p File name Edge _AAL90_Binary edge m Files of type Edge files edge Cance Fig 7 Select an edge file AAL90 binary file is selected Edge AAL90 Binary edge Notepad File Edit Format View Help OOH POOH POOOOOOOOHP POOOOOoomnmooc OOOOoOoOooooooom oooooooooomnm OOOOoOOoOoOOHPOOOOOOOOOPOOOOOO OOOOoH POOOHPOOOOOOOOOPOOOOPMO OOH POoOH POOOOOOOOOOOOOP POOOooo OOH PoOoOOOHPOOOOOOOOOOOOOOOOO OOH POHPOOOOOOOOOOOOOPOOOOOO OOOOooOooooooooom ooooooooomo OOoOooooP Poooooomp ooooooooooo Fig 8 Edge file AAL90 Binarized Both node and edge files can be generated edited with text editors or Excel 4 4 Load a volume file This function lets users map the volume data to the brain surface The volume file should be a NIFTI paired file which could be T map Z map atlas or any other volume data BrainNet Viewer User Manual 1 0 July 11 2011 Selecting either hdr or img file is acceptable When choosing to map volume images the edit boxes f
22. v and Colin27 Data SurfTemplate BrainMesh_ch2 nv and separate hemisphere surfaces Data Surffemplate ICBM152Left nv ICBM152Right nv In the below example the ICBM152 template is selected Fig 4 BrainNet Viewer User Manual 1 0 July 11 2011 Load Files BP Load File fol c 28 i onm Data file node Browse Data file edge Browse Volume file Browse mum B Select File to Open Lookin jj SufTemplte e amp ekEE Name Date modified amp BrainMesh_ch2 nv 2010 12 30 13 18 BrainMesh_ICBM152 nv 2011 3 29 12 27 Ww amp ICBM152Left nv 2011 5 10 12 22 Desktop amp ICBM152Right nv 2011 5 10 12 24 mb Recent Places 4 File name BrainMesh_ICBM152 nv v Files of type Net Viewer Files nv w The information below is about the definition of the surface Type NV File NV File NV File NV File p Cancel Fig 4 Select brain surface ICBM152 is selected file Usually you don t need to generate a new surface file Please read the file if interested or if you want to make a surface by yourself The brain surface file is defined as an ASCII text file with suffix nv and contains four fields 1 Vertex number 2 Vertex coordinate 3 Triangle faces number 4 Index of vertex making up the triangles The ICBM152 brain surface was derived from Freesurfer http surfer nmr mgh harvard e
23. xit Click to exit BrainNet Viewer 20 BrainNet Viewer User Manual 1 0 July 11 2011 6 2 Option Option Click to open the option panel see more details in section Visualize Option Load Option Load a previously saved visualize option file Save Option Save current visualize option as a mat file 6 3 Visualize Redraw Clear figure and redraw network using the data and option last loaded Clear Figure Remove brain network and display the default information of BrainNet Viewer 6 4 Tools Merge Mesh This tool is used to merge the left and right hemisphere surface files extracted from FreeSurfer pial or BrainVISA mesh from two separate files into one BrainNet Viewer surface template file nv or to convert a one hemisphere surface file to a BrainNet Viewer surface template file nv When both Left Mesh and Right Mesh files are selected the new mesh will combine two hemisphere files into one file If only one of the input files is selected the new mesh file will convert only that hemisphere file Fig 20 m Merge Meshes o 2 Merge Files Left Mesh Browse Right Mesh Browse New Mesh Browse ne Fig 20 Merge Meshes tool 21 BrainNet Viewer User Manual 1 0 July 11 2011 6 5 Help Manual Open this manual for help About Show version author and contact information of BrainNet Viewer in a dialog

BrainNet Viewer Manual (PDF version, 1M)

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