Visualize JLF ROIs with BrainNet Viewer - PennBBL/pncT1Bifactors GitHub Wiki

Author: Antonia Kaczkurkin
Date: 11/28/2018
Replicator:
Goal: To generate brain images using BrainNet Viewer (a software application used to view structures in 3D).

Create a file with a list of the significant t-values and atlas index numbers

  1. Use the script /data/jux/BBL/projects/pncT1AcrossDisorder/scripts/KaczkurkinPark_BifactorStructure/GamAnalyses_T1Bifactors_JLFct.R or /data/jux/BBL/projects/pncT1AcrossDisorder/scripts/KaczkurkinPark_BifactorStructure/GamAnalyses_T1Bifactors_JLFvol.R to:
    a. Load the subject data and JLF atlas labels
    b. Run GAM models with the JLF ROIs
    c. Pull the FDR-corrected significant ROI names and t-values into a data frame
    d. Merge with the JLF atlas file to add index numbers that correspond to the significant ROIs
    e. Save just the t-values and index numbers as a .csv file

Create an image with t-values assigned to each significant region

  1. Use the function AssignTValueToAtlas.m to assign the significant t-values to the JLF atlas for input into BrainNet Viewer.

First, make sure your atlas is in .nii format (not .nii.gz).

   fslchfiletype NIFTI *.nii.gz

Run the function AssignTValueToAtlas but check that the paths are correctly specified in /data/jux/BBL/projects/pncT1AcrossDisorder/scripts/KaczkurkinPark_BifactorStructure/Run_AssignTValueToAtlas_*.m before running.

   matlab -nodesktop

   Run_AssignTValueToAtlas_ctFear

OR

   Run_AssignTValueToAtlas_volMood

OR

   Run_AssignTValueToAtlas_volOverall

This will output an image file (e.g. JLFct_signifROIs_fear.nii) in the folder you specified.

  1. Use the function SetColormap.m to create a custom color palette. Check that the paths are correctly specified in /data/jux/BBL/projects/pncT1AcrossDisorder/scripts/KaczkurkinPark_BifactorStructure/Run_SetColormap_*.m and run.
   matlab -nodesktop

   Run_SetColormap_ctFear

OR

   Run_SetColormap_volMood

OR

   Run_SetColormap_volOverall

This will output the colormap file (e.g. blues_ctFear.txt) in the folder you specified.
3. Download BrainNet Viewer from https://www.nitrc.org/frs/?group_id=504 or use the copy on server located here: /data/jux/BBL/projects/pncT1AcrossDisorder/BrainNetViewer_20171031

  1. To open BrainNet Viewer on the server:
   cd /data/jux/BBL/projects/pncT1AcrossDisorder/BrainNetViewer_20171031

   matlab -nodesktop

   BrainNet

  1. The BrainNet Viewer GUI will open.
    a. File -> Load File
    b. Surface: Select /data/jux/BBL/projects/pncT1AcrossDisorder/BrainNetViewer_20171031/Data/SurfTemplate/BrainMesh_ICBM152.nv
    c. Mapping: Select /data/jux/BBL/projects/pncT1AcrossDisorder/images/JLF_ct/JLFct_signifROIs_fear.nii
    d. Ok

  2. The BrainNet_Option box will open.
    a. Layout: Choose Full View
    b. Volume: ROI drawing
    c. Volume: Next to "Color" click on the Load button (choose /data/jux/BBL/projects/pncT1AcrossDisorder/images/JLF_ct/blues_ctFear.txt d. Ok

  3. Save image
    a. File -> Save Image
    b. File -> Exit