Tutorial: Brain Surface

Catalog

• 1 Getting started

• 2 Contacts

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1 Getting started

1. Data Prepare

   (1) Prepare a .txt file with 160 rows and m columns. Elements in one row are split by space. Each element can be an integer or float number.

   Example: file data/example.txt. Here m=1 and data type is float.

   Hint: you can call the build_txt() function in utils.py to easily generate such txt file from an array (or list) in (160,-1) shape.

2. Build .vtk file

   (1) In a Windows terminal, cd to this repo's root directory, then

   $ .\bin\Network2DestrieuxSurfaceRendering.exe .\bin\icbm_avg_mid_sym_mc_right_hires.vtk ${YOUR_INPUT_TXT_PATH} ${YOUR_RIGHT_OUTPUT_TXT_PATH_WITHOUT_SUFFIX} -V .\bin\Atlas_Right_Destrieux.txt -R .\bin\RightROI2NodeLookupTable.txt -m ${THE_COLUMN_NUMBER_M}
   $ .\bin\Network2DestrieuxSurfaceRendering.exe .\bin\icbm_avg_mid_sym_mc_left_hires.vtk ${YOUR_INPUT_TXT_PATH} ${YOUR_LEFT_OUTPUT_TXT_PATH_WITHOUT_SUFFIX} -V .\bin\Atlas_Left_Destrieux.txt -R .\bin\LeftROI2NodeLookupTable.txt -m ${THE_COLUMN_NUMBER_M}

   Example:

   $ .\bin\Network2DestrieuxSurfaceRendering.exe .\bin\icbm_avg_mid_sym_mc_right_hires.vtk .\data\example.txt .\output\example_right -V .\bin\Atlas_Right_Destrieux.txt -R .\bin\RightROI2NodeLookupTable.txt -m 1
   $ .\bin\Network2DestrieuxSurfaceRendering.exe .\bin\icbm_avg_mid_sym_mc_left_hires.vtk .\data\example.txt .\output\example_left -V .\bin\Atlas_Left_Destrieux.txt -R .\bin\LeftROI2NodeLookupTable.txt -m 1

   (2) Then the output .vtk file will be generated in the given output path, like file output/example_right_1.vtk and output/example_left_1.vtk).

3. Install App ParaView

   (1) Home page: https://www.paraview.org/

   (2) Click "DOWNLOAD"

   (2) Download and install "ParaView-5.11.0-Windows-Python3.9-msvc2017-AMD64.msi"

4. Operations in ParaView

   (1) File -> Open ... (choose the .vtk files)

   Hint: you can open multiple .vtk files at a time. Click the "eye" button near the .vtk file's name to make it visible (or invisible)

   (2) Hide the XYZ axis label

   (3) Make screenshots

2 Contacts

Please email chenm@wfu.edu