BrainNet Viewer Manual 1.41 (PDF version, 2M)
Contents
1. Load Files Surface file Browse Data file node Browse Data file edge Browse Volume file Browse m O pes 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 several brain surfaces based on two different brain templates ICBM152 BrainNet Viewer User Manual 1 41 September 18 2012 Data Surffemplate BrainMesh_ICBM152 nv and Colin27 Data SurfTemplate BrainMesh_ch2 nv and separate hemisphere surfaces Data Surffemplate ICBM152Left nv ICBM 152Right nv In the below example the ICBM152 template is selected Fig 4 a Load File o Load Files Surface file Q Browse Data file node Data file edge Browse Volume file Browse Look in SurfTemplate e Na Name amp BrainMesh ch2 nv 2010 12 30 13 18 Ww di ICBM152Left nv 2011 5 10 12 22 Desktop Gf ICBMIS2Right nv 2011 5 101224 NV File 4 n 3 Fle gee BrainMesh_ICBM152 nv Files of type Net Viewer Files nv Cancel Fig 4 Select brain surface ICBM152 is selected The information below is about the definition of the s2. Custom Show the brain in a custom viewpoint defined by azimuth and elevation see more detail of function view in Matlab help 13 BrainNet Viewer User Manual 1 41 September 18 2012 Medium view Show lateral and medial side of each hemisphere in the figure The top row contains lateral view of left and right hemispheres while the bottom row contains medial view of left and right hemispheres Full view Show six or eight depending on whether the brain surface can be divided into left and right hemispheres brain models In the six brain mode the top row from left to right are left side top side and frontal side while the bottom row from left to right are right side bottom side and back side In the eight brain mode the first row from left to right are lateral view of left hemisphere top side lateral view of right hemisphere the second row from left to right are medial view of left hemisphere bottom side medial view of right hemisphere and the third row are frontal side and back side See Fig 11 Single View Custom Az 130 El 30 Medium View Full View six brain Full View eight brain Fig 11 Different layouts 14 BrainNet Viewer User Manual 1 41 September 18 2012 5 2 Global panel The global panel provides several options for global figure adjustment Fig 12 Background Color Change the color of the background Right click on the color square right beside the text Background Color and select
3. 6 Surface mapping ges 7 Surface mapping amp 8 Surface mapping 9 ROI in Volume node with node amp edge Fig 2 Brain network pictures with the BrainNet Viewer BrainNet Viewer User Manual 1 41 September 18 2012 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 including 1 Colin brain inflated Colin brain Colin brain with cerebellum ICBM152 brain MNI Talaraich smoothed ICBM152 brain MNI Talaraich hemispheres of ICBM152 and hemispheres of smoothed ICBM152 brain surface in the folder Data SurfTemplate and 2 node and edge files for Automated Anatomical Labeling AAL 90 regions Tzourio Mazoyer et al 2002 Brodmann areas 82 regions Brodmann 1909 Harvard Oxford Atlas HOA 112 regions Smith et al 2004 ROIs defined by Dosenbach et al 160 ROIs Dosenbach et al 2010 ROIs defined by Fair et al 34 ROIs Fair et al 2009 LONI Probabilistic Brain Atlas 40 regions Shattuck et al 2008 and others e g customized ROIs by users in the folder Data ExampleFiles Load File ol m JI
4. HOA112 Dos160 Fair34 LPBA4O 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 BBP Load File o amp s Load Files Surface file Browse Data file edge Browse Volume file Browse Reset OK Cancel BrainNet Viewer User Manual 1 41 September 18 2012 r Select File to Open Look in AAL90 Name Date modified Type d Node AAL90 nod o 2001 9 3111 06 NODE File Recent Places Sw NODE AALIO node 5 31 11 06 NODEFile uw Desktop Libraries f Computer Network 4 m p File name Node_AAL90 node v Files of type Node files node Cancel Fig 5 Select node file AAL90 is selected The node file is defined as an ASCII text file with the suffix node In the node file there are 6 columns columns 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 inf
5. 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 29 BrainNet Viewer User Manual 1 41 September 18 2012 Print panel Zoom in amp Zoom out Fig 23 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 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 30 BrainNet
6. Viewer User Manual 1 41 September 18 2012 Sagittal View Axial View Coronal View Fig 24 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 31 BrainNet Viewer User Manual 1 41 September 18 2012 Acknowledgements We thank the following colleagues for their kind helps during BrainNet Viewer developing and manual revising Dr G Gong Dr N Shu Dr C Yan Mr J Wang Mr T Xie Mr Q Lin Ms Z Dai Ms M Cao and Ms J Zhang National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University China Professor A Evans McGill University Canada Mr P Clark Pennsylvania State University USA Mr M Ghasemi Tarbiat Modares University Iran We also thank the developers of the following softwares and toolboxes whose source codes or file formats were referenced during our package developing Matlab www mathworks com products matlab SurfStat www math mcgill ca keith surfstat FreeSurfer http surfer nmr mgh harvard edu BrainVISA http brainvisa info SPM www fil ion ucl ac uk spm This work was supported by the Natural Science Foundation of China Grant Nos 81030028 and 30870667 and Beijing Natural Science Foundation Grant No 7102090 32 BrainNet Viewer User Manual 1 41 September 18 2012 Reference Brodmann K 1909 Verglei
7. 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 m Load File S m EJ Load Files Surface file Browse Data file node Browse Data file edge Volume file Browse 5 Select File to Open rem hau ANO o A Name Date modified 7 Edge AAL90 Binary edge eir EN amp Edge AAL90 Weighted edge n File name AALSO Binary edge v Files of type Edge files edae 2011 4 14 14 25 2011 4 14 14 23 Type EDGE File EDGE File r Edge AAL90 Binary edge Notepad File Edit Format View Help 0 OOH POOHPOOOOOOOOr Pooooooomrmococ OOOOooOoooooooom Poooooooooomnm OOOOHP POOOHPOOOOOOOOOP PoOoOoOooomo OOH PoOP POOOOOOOOOOOOOPOOOOOO OOOOOOOoOoH POOooooooor Pooooo OOH POOOOHPOOOOOOOOOOOOOOOOO OOH POHPOOOOOOOOOOOOoOOoOr Poooooo OOOOooOooooooooom ooooooooomo OOOOoOoOoHP POOOOOooP Pooooooooooo Fig 8 Edge file AAL90 Binarized BrainNet Viewer User Manual 1 41 September 18 2012 11 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 NIFTI format which could be T map Z map atlas or any other vol
8. value Nodal module assign edge color according to the color of nodes it links If two nodes of the edge have same color the edge will be set as the same color If the two nodes are with different color the edge will be colored gray Absolute value use absolute value in matrix to calculate edge color 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 or draw ROI volume in brain surface The volume file could be a T map Z map an atlas image etc E z BrainNet Option Layout a Volume Global Type Selection Surface Node Volume to surface RO drawing Edge Image Volume mapping Volume Data Range 0 00 116 00 Display Positive only v Positive Range 0 00 116 00 li 0 01 10 00 Color for Null Map algorithm Interpolated X Colormap AFNI X v Adjust for null ROI drawing Fig 16 Volume panel Type Selection select to map volume to brain surface or draw ROI volume in brain surface Volume mapping zone 22 BrainNet Viewer User Manual 1 41 September 18 2012 Volume Data Range show the minimum and maximum values of the volume file Display contain three mapping manner Positive amp Negative Positive only and Negative only Positive amp Negative sets the colorbar range from the minimum negative val
9. voxel Minimum voxel Extremum voxel Map algorithm Fig 17 Volume mapping ROI drawing zone Please ensure your volume data is arranged with natural number index ROI Index Range show the minimum and maximum index of the volume file number 0 is out of use Draw All construct and draw each ROI volume in sequence according to their index Custom input the index number of ROIs these ROIs will be selected to reconstruct and 24 BrainNet Viewer User Manual 1 41 September 18 2012 draw Color set the color of each ROI volume Smooth smooth the surface of ROI volume Fig 18 ROI volume drawing 5 7 Image panel 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 19 F B option Layout image Size Background Pixel Dimensions Surface Node Width 2000 Edge Volume Height Image ig 1500 r Document Size Width 16 93 cm Height 12 70 cm DPI 300 Constrain Proportions Fig 19 Image panel 25 BrainNet Viewer User Manual 1 41 September 18 2012 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 ols After visualization click here to save the present figure as an image At present
10. 0 1 10 Color same M cooma Jet Modular Threshold 1 00 i Load Save Reset OK Z Cancel Fig 14 Node panel 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 Value 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 Equal set all nodes to an equal size ignoring the size value in the file and the size can be defined in the edit box 18 BrainNet Viewer Use
11. 2012 1 Introduction Please cite as lt was were visualized with the BrainNet Viewer http www nitrc org projects bnv while using the package to make publicized pictures BrainNet Viewer is a brain network visualization tool 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 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 41 September 18 2012 2 Installation 2 1 Run BrainNet Viewer on a PC with Matlab Run Matlab A version of R2010b or above is recommended Add BrainNet Viewer path to Matlab search path 1 Type Addpath X BrainNet where X BrainNet refers to the path of BrainNet Viewer on the machine Or 2 Click File in Matlab menu Click Set Path gt Click Add with Subfolders button in the popup dialog gt Select the BrainNet Viewer folder on the machine gt Click OK button gt Click Save Button Run
12. BrainNet m Type BrainNet in the command window of Matlab 2 2 Run BrainNet Viewer on a PC without Matlab Please contact us if you need standalone version It cannot be found on the NITRC due to the large size Install Matlab Components Runtime MCRInstall exe for Windows OS or MCRInstaller bin for Linux and Mac OS 200MB using default settings Restart your computer strongly recommended Run BrainNet exe for Windows OS or run BrainNet sh for Linux and Mac OS it should take about one minute to start You can find the interface below Fig 1 after successfully running the BrainNet Viewer BrainNet Viewer User Manual 1 41 September 18 2012 jf BrainNet Viewer ji File Option Visualize Tools Help E s o9e9 ecaoab tm BrainNet Viewer Version 1 0 RC 1 A flexible and rapid network mapping tool National Key Laboratory of Cognitive Neuroscience and Learning CE ex b i Beijing Normal University TAS Contact Infomation Mingrui Xia mingruixia gmail com Yong He yong h he gmail com Fig 1 The interface of BrainNet Viewer BrainNet Viewer User Manual 1 41 September 18 2012 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 7 8 9 Brain surface load brain surface file only See secti
13. C 8107 T hdr 2011 5 6 14 37 HDR Fi 4 n File name Pos_AD NC_ROI01_Timg Files of type All Files v Cancel Fig 9 Volume file a paired NIFTI file of T test Map is selected 12 BrainNet Viewer User Manual 1 41 September 18 2012 5 Visualize option The option panel has three parts Fig 10 The list box on the left includes Layout Global 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 to acquire or save options as a mat file Reset to return all parameters to their original state OK to draw graph and close option panel Apply to draw graph but keep option panel and Cancel to exit the panel without changes z BrainNet Option Layout Single view View direction Sagittal Axial Coronal Custom Medium view Full view L9 jJ LS Fig 10 Option panel 5 1 Layout panel This panel is used to set the output view of the brain model Single view Show only one brain model in the figure Sagittal Show the brain in sagittal view left side Axial Show the brain in axial view dorsal side Coronal Show the brain in coronal view frontal side
14. TIFF BMP EPS JPEG and PNG image formats 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 20 Frames of the network movie Exit Click to exit BrainNet Viewer 26 BrainNet Viewer User Manual 1 41 September 18 2012 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 Colormap Editor Call colomap editor to edit colormap manually Apply Colormap Apply edited colormap by colormap editor to all graphs in figure Save Colormap save colormap as a text file The saved colormap can be used by copy its text into cus
15. chende lokalisationslehre der grobhirnrinde Barth Leipzig Dosenbach NU Nardos B Cohen AL Fair DA Power JD Church JA Nelson SM Wig GS Vogel AC Lessov Schlaggar CN Barnes KA Dubis JW Feczko E Coalson RS Pruett JR Jr Barch DM Petersen SE Schlaggar BL 2010 Prediction of individual brain maturity using fMRI Science 329 1358 1361 Fair DA Cohen AL Power JD Dosenbach NU Church JA Miezin FM Schlaggar BL Petersen SE 2009 Functional brain networks develop from a local to distributed organization PLoS Comput Biol 5 e1000381 Shattuck DW Mirza M Adisetiyo V Hojatkashani C Salamon G Narr KL Poldrack RA Bilder RM Toga AW 2008 Construction of a 3D probabilistic atlas of human cortical structures Neuroimage 39 1064 1080 Smith SM Jenkinson M Woolrich MW Beckmann CF Behrens TE Johansen Berg H Bannister PR De Luca M Drobnjak Flitney DE Niazy RK Saunders J Vickers J Zhang Y De Stefano N Brady JM Matthews PM 2004 Advances in functional and structural MR image analysis and implementation as FSL Neuroimage 23 Suppl 1 9208 219 Tzourio Mazoyer N Landeau B Papathanassiou D Crivello F Etard O Delcroix N Mazoyer B Joliot M 2002 Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single subject brain Neuroimage 15 273 289 33 BrainNet Viewer User Manual 1 41 September 18 2012
16. e 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 another 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 19 BrainNet Viewer User Manual 1 41 September 18 2012 z BrainNet Option Layout m Edge Global Draw Edge Surface Node Draw All Volume Image _ Above Threshold 0 00 Sparsity 0 10 V Absolute value Inter Hemi Edges Directed 526 Value Auto v Equal 1 00 E Threshold 0 00 V Absolute value i Scale gt 1 00 x Range 0 1 10 Color Same n Colormap Jet V Absolute value Threshold m nodal module Length mm 0 m L R e jy NN 72 E MI eS LL o vi p F elf fA b 4 a NN P Af RT A jJ hy A v 4 Fig 15 Edge panel and directed network Image data is from M Ghasemi Tarbiat Modares university Tehran Iran 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 Draw All extract and draw all ed
17. ges all values not equal to zero in the correlation matrix Threshold extract the edge above a threshold This threshold can be set as a value in the matrix or in the sparsity of the matrix Absolute value use absolute value to extract edges from the matrix Inter Hemi Edges extract edges that travel across two hemispheres Directed draw edges with direction 20 BrainNet Viewer User Manual 1 41 September 18 2012 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 in undirected mode Always remember 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 Value 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 Equal set all edges
18. information and adjust with your own data at the end of the file The first half would be placed in the brain model on the left and the last half would be placed in the brain model on the right For instance an original AAL90 node file includes 90 rows they will be shown on the left Then copy them and paste as the row 91 to 180 this part would be shown on the right Edge file the edge file includes intra and inter brain association matrix For instance the original AAL90 edge file includes a 90 X 90 matrix In the double brain model please 16 BrainNet Viewer User Manual 1 41 September 18 2012 arrange an edge file with 180 X 180 matrix in which the matrix 1 90 1 90 and 91 180 91 180 are intra connections of each brain and 1 90 91 180 and 91 180 1 90 are inter connections between the two brains Bee 0000000000000 lei E Double Brain Fig 13 Surface panel and double brain model 5 4 Node panel There are four zones in this panel to control node drawing label setting nodal size and nodal color separately 17 BrainNet Viewer User Manual 1 41 September 18 2012 Bl option oll m s Layout Node Background r Draw Nodes Surface Draw All Edge Volume image Above Threshold gt 200 size Label Label All Label None Font Above Threshold 2 00 Size Size Value Auto v Equal 3 00 Threshold 2 00 Scale E LI i 0 70 x Range
19. l Set the level of object detail by adjusting the numbers of vertex of nodes and edges when drawing a graph theoretical network figure High default Moderate and Low 15 BrainNet Viewer User Manual 1 41 September 18 2012 r gt S s BrainNet Option Ecos ni eic Shiny Dull Metal Custom 0 5 0 5 0 5 Global setting Object material a P Flat Faceted Interp Shading properties Flat Gouraud Phong None Background Color Object Material Dull v 0 5 Shading properties interp Lighting algorithm Phong E Light direction Right Y Renderer OpenGL ae Graph detail High v Lighting algorithim TL ate snr Load Save Reset OK Apply Cancel 7 j Py N AU 2 m CAD A Headlight Right Left Light direction Fig 12 Global panel 5 3 Surface panel This panel is used to adjust properties of the brain mesh Color right click the color square and select required color in the popup dialog to change color of the brain surface Opacity drag the slider bar or enter a number range from 0 1 in the edit box to change the transparency of the brain surface Double Brain click to display two brain models in one figure usually used to display the relationship between nodes in two time points To display such figure please arrange node and edge files as follow Node file duplicate the node
20. null Colormap provide 24 kinds of colormaps including custom colormap Map algorithm eight mapping algorithms are provided Nearest Voxel assign the vertex with the value of voxel in volume that is nearest to it suitable for atlas and mask Average Vertex assign the vertex with the value of voxel in volume that is nearest to it then average the vertex across its neighbors time costly Average Voxel assign the vertex with the average value of voxel and its neighbors in volume that is nearest to it Gaussian the volume is first snoothed by a Gaussian kernel and then assign the vertex with the value of voxel in volume that is nearest to it Interpolated default the coordinate of the vertex is determined in the volume trilinear interpolate method is then used across its neighbors to calculate the value Maximum Voxel assign the vertex 23 BrainNet Viewer User Manual 1 41 September 18 2012 with the maximum value of voxel and its neighbors in volume that is nearest to it Minimum Voxel assign the vertex with the minimum value of voxel and its neighbors in volume that is nearest to it Extremum Voxel assign the vertex with the extremum value of voxel and its neighbors in volume that is nearest to it Positive amp Negative Positive only Negative only Colormap Jet Colormap Hot Colormap Winter Display Nearest voxel Average vertex Interpolate Maximum
21. on 4 1 for file preparation and section 5 3 for visualization options Nodes load node file only See section 4 2 for file preparation and section 5 4 for visualization options Brain surface and nodes load both brain surface and node files See sections 4 1 and 4 2 for file preparation and section 5 3 and 5 4 for visualization options Nodes and edges load both node and edge files See sections 4 2 and 4 3 for file preparation and section 5 4 and 5 5 for visualization options Brain surface nodes and edges load brain surface node and edge files together See sections 4 1 to 4 3 for file preparation and section 5 3 to 5 5 for visualization options Volume mapping to surface load brain surface and volume files See section 4 1 and 4 4 for file preparation and section 5 3 and 5 6 for visualization options Volume mapping to surface and node load brain surface node and volume files See section 4 1 4 2 and 4 4 for file preparation and section 5 3 5 4 and 5 6 for visualization options Volume mapping to surface with node and edge load brain surface node edge and volume files See section 4 1 to 4 4 for file preparation and section 5 3 to 5 6 for visualization options ROI cluster drawing in volume load brain surface and volume files See section 4 1 and 4 4 for file preparation and section 5 3 and 5 6 for visualization options BrainNet Viewer User Manual 1 41 September 18 2012 5 Surface Nodes amp 4 Nodes amp Edges
22. oo c D N c O N UO Y i QD cc n e c 29 Y L gt Contents t MOU CUON e 2 DZ MVS CANA ON m E AE E E A E E EE EE T 3 2 1 Run BrainNet Viewer on a PC with Matlab 3 2 2 Run BrainNet Viewer on a PC without 21 3 dii e 5 ZEE AG FW 7 i EN Eoo E SUIT Ce TI RTT ET ETT 7 42 viter dietro NoD V Der 9 A POAC AN COPS TNC OTRO A 10 4 4 Load a volume file ssccccessesccrensescerensescerensesceseasescereneesceneassscerssssscarasssscees 12 ERU rd Re erm 13 S M E E o a e E A A I A E E E 13 S GODO 1 eara E E EE AEE EATE 15 o SUCEDE Emm 16 92922 17 SS Ede DNE e a EE EE E E E 19 20 Voume PIN PN m 22 D 7 Insee DalBl aeneum E E E E EE E E 25 o rr S 26 i 26 OO 27 Oo sa ee 27 GO 27 6 5 28 DO 29 74 LoadfilesS SAVE ds 558 ee 29 Loan 29 7 3 Move Rotate amp Get position pe 30 LA SUA AUG VIEW E TTE 30 31 32 PROTON CIC arent mises 33 1 BrainNet Viewer User Manual 1 41 September 18
23. ormation 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 41 37 8 21 52 09 18 45 34 81 42 2 21 9 31 12 43 82 16 56 47 32 13 31 18 49 48 1 14 02 33 43 32 73 35 46 37 59 33 06 34 04 30 65 50 43 9 62 33 18 52 59 10 73 48 43 12 73 19 02 50 2 14 98 21 41 45 58 29 91 13 99 50 33 30 16 14 17 35 98 30 71 12 11 41 22 32 23 11 91 47 16 8 48 13 95 52 65 6 25 14 63 5 32 4 85 61 38 8 62 0 17 61 85 8 06 15 05 11 46 10 43 15 91 11 26 4 8 49 17 30 89 9 1 50 84 30 22 5 17 54 06 7 4 A e eeuk us FP HF Ww uw UJ UJ UJ UJ UJ UJ UJ UJ 9 P I I PreCG R SFGdor R n ORBsup R MFG L MFG R ORBmid L ORBmid R IFGOperc L IFGOperc R IFGtriang L IFGtriang R ORBinf L ORBinf R ORBsupmed L Fig 4 3 Load an edge file 6 Node file AAL90 The brain edge file is defined as an ASCII text file with suffix edge representing a connectivity e g correlations matrix among the ROls which could be weighted or BrainNet Viewer User Manual 1 41 September 18 2012 10 binarized and therefore the dimensions of the matrix must correspond to the number of nodes AAL90 Brodmann82 HOA112 Dos160 Fair34 LPBA4O and other e g customized ROls by users files are
24. r Manual 1 41 September 18 2012 Scale 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 nodal color Same 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 gm ae B EU EE Hel Colormap use a color map to display the value of the nodes from low BENE sorro end to high end corresponding to column 4 in the node file 13 kinds of color maps can be selected see the right picture for detail Mid Eus Modular modular color can be used to display different nodal colors modet B for different modules Set the values of column 4 as 1 2 3 A corresponding to modular 1 modular 2 in the node file The Module3 9 maximum number of modules is21 at present Click to open the was W modular color dialog and the left picture will display six modules woe ag with their color on the right Click the popup menus on the left to OK Cancel select other modules in the list and the color square will change to the corresponding one Right click the color square to change color as described above Threshold 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 th
25. the desired color in the popup dialog Object Material Provide four manner to define material of the mode in figure Shiny Dull default Metal and Custom which the ambient diffuse and specular can be freely defined Shading properties Set color shading properties Flat Faceted and Interp Flat each triangle of the mesh has a constant color appropriate for atlas or ROI display Faceted show edges of the mesh Interp varies the color of triangle by interpolating the colormap appropriate for functional connectivity ALFF ReHo or any volume with continuous data default Lighting algorithm Set lighting algorithm Flat Gouraud Phong and None Flat produces uniform lighting across each of the faces of the object Gouraud calculates the vertex normals and interpolates linearly across the triangles Phong interpolates the vertex normals across each face and calculates the reflectance at each pixel Better but costly than Gouraud default None turn off light Light direction Set where the light comes from Headlight Right default and Left Renderer Set the render method OpenGL default and zbuffer Texts displayed are sometimes upside down with some type of AMD ATI graphic cards when using OpenGL mode Turn this option to zbuffer would solve this problem However the image is saved with texts in right direction Graph detai
26. to an equal size and the size can be defined in the edit box Scale the scale option is used to adjust the size of all edges together The scale factor ranges from 0 1 to 10 Absolute value use absolute value in matrix to calculate edge radius Edge color This panel provides five ways to control edge color Same adopt the same color for all edges right click the color square and select the required color from the popup dialog Colormap 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 Threshold binarize the color by a given threshold drag the slider bar or enter the 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 lower value while the right one represents the higher value 21 BrainNet Viewer User Manual 1 41 September 18 2012 Length 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
27. tom colormap in option panel 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 21 27 BrainNet Viewer User Manual 1 41 September 18 2012 B Merge Meshes fo m 2 Merge Files Left Mesh Browse Right Mesh Browse New Mesh Browse mium amni amnium Fig 21 Merge Meshes tool 6 5 Help Manual Open this manual for help About Show version author and contact information of BrainNet Viewer in a dialog BrainNet Viewer User Manual 1 41 September 18 2012 7 Toolbar The toolbar Fig 22 provides frequently used and interaction commands to operate the brain network graph most of them are not included in the menu TELESERIAL Fig 22 Toolbar 7 1 Load Files amp Save as
28. ue to the maximum positive value and Positive only and Negative only just set the range of the colorbar in positive value or negative value separately Positive Range and Negative Range 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 Color for Null define the color for null value part on the surface Right click the color square and select required color Adjust for Null when this option is selected the colormap will be adjusted for null value vertex Specifically in Positive amp Negative mode the vertex with value between high end of negative interval and low end of positive interval will be set as color for null in only positive mode the vertex with value below the low end of positive interval will be set as color for null and in only negative mode the vertex with value larger than the low end of positive interval will be set as color for
29. ume data either paired files or nii file are accepted Besides a text file containing ann X 1 vector is accepted in which n equals to the vertex number of the brain surface 81924 vertexes in ICBM whole brain surface The principle of volume mapping is to transfer the vertex coordinates on the brain surface to the voxels in the image file using different algorithms and assign vertices to corresponding values The principle of ROI drawing is to reconstruct voxels with same index in the image file to 3D volume m Load File o Jf amp is r Load Files Surface file Browse Data file node Browse Data file edge Browse Volume file Reset OK Cancel Select File to Open Look in Ji Res er Exe Name Date modified Type mecat hnes posADNCROmLTa o 2011 5161437 HORF e Pes ADNC ROD Timg araea GE Ww Pos AD NC ROIO02 T hdr 2011 5 6 14 37 HDR Fi Desktop 4 Pos AD NC ROID2 T img 2011 5 6 14 37 IMG Fi Pos AD NC ROIO03 T hdr 2011 5 6 14 37 HDR Fi a 4 Pos AD NC ROIO3 T img 2011 5 6 14 37 IMG Fi Libraries Pos AD NC_ROI04_T hdr 2011 5 6 14 37 HDR Fi A 4 Pos AD NC ROID4 T img 2011 5 6 14 37 IMG Fi Es Pos AD NC ROIO05 T hdr 2011 5 6 14 37 HDR Fi Computer po AD NC ROIDS T img 2011 5 6 14 37 IMG Fi Tw Pos AD NC_ROI06_T hdr 2011 5 6 14 37 HDR Fi N f Pos AD NC ROIO6 T img 2011 5 6 14 37 IMG Fi amp Pos AD N
30. urface 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 edu and the Colin27 brain surface was made by BrainNet Viewer User Manual 1 41 September 18 2012 BrainVISA http brainvisa info We transferred and merged the original bilateral hemisphere files into one nv file A surface merge tool is in the tools menu see more details in section 6 4 Menus Tool Currently the pial files generated by FreeSurfer only hemisphere mesh and the 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
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