Figure Maker

It can often be difficult to standardize the way figures are made in the connectome workbench view. Furthermore, workbench does not have an easy way to generate brain images automatically from the command line. Nobody wants to manually create thousands of images. The figure maker is a python wrapper for a bash script (make_dscalar_pics_vX.X.sh). The script uses a template scene file and uses a(n exhausting) list of sed commands to replace the file names and parameters within the scene file to generate an image file.

On MSI, the code can be found at /home/faird/shared/code/internal/utilities/figure_maker. There is a README in this directory that includes more information about installation and dependencies.

You can find the version-controlled code on gitlab.

Here is an example of a valid call to this script:

python3 ./figure_maker_wrapper.py --subject-scalar ./group1_dscalar_AVG.dlabel.nii --output ./output/figure.png --label-lower -1 --label-upper 1 --threshold-image --threshold-lower 0 --threshold-upper 10

Basic Arguments

  • These arguments can be given in any order.
  • The --subject-scalar argument is the only argument that is always required.
  • If the --label flag is included, its lower and upper bound arguments must also be included. Otherwise, the bound arguments are unneeded. The same applies to the required arguments with the word threshold.
Flag Default Description of Argument
--subject-scalar N/A Required. Path to subject dscalar or dlabel file.
--output ./figure.png Path to output image file. By default, it will be a .png file.1
--label-lower Depends on dscalar vs. dlabel Lower scale limit for color pallet.
--label-upper Depends on dscalar vs. dlabel Upper scale limit for color pallet.
--palette-name ROY-BIG-BL Supply the name of the color palette. All of the color palette options are listed below.2
--threshold-image N/A (FALSE) Include this flag if you want to exclude data inside or outside of a specific threshold.
--threshold-lower Depends on dscalar vs. dlabel Lower threshold for color pallet.
--threshold-upper Depends on dscalar vs. dlabel Upper threshold for color pallet.
--threshold-inside THRESHOLD_TEST_SHOW_OUTSIDE Include this flag to set data exclusion threshold to THRESHOLD_TEST_SHOW_INSIDE instead of THRESHOLD_TEST_SHOW_OUTSIDE.
--make-quad N/A (FALSE) Include this flag to make DV view. By default, it won't.
--make-subcorticals FALSE Include this flag to create new images that show parasaggital, coronal, and axial views.
--width-in-cm 8 Width in centimeters of the final image.
--dots-per-cm 118 Dots per centimeter (dpcm) in the final image. The default value, 118, will give 300 dots per inch (dpi).
--save-scene-file N/A (FALSE) Include this flag to save the scene file. Helpful for debugging.
--wb-command (Depends on server) Path to workbench command file (wb_command). Default depends on which server the script is run from.

For more advanced arguments, see the README in /home/faird/shared/code/internal/utilities/figure_maker