Compute tractography measures using Slicer FiberTractMeasurements module

fibertractmeasurements_slicerpy_anon.py

# -*- coding: utf-8 -*-

import subprocess

#import slicer
#from slicer.ScriptedLoadableModule import *


def run_command(command, out_path):

    out_fp = open(out_path + "stdout.txt", "w")
    err_fp = open(out_path + "stderr.txt", "w")
    exit_code = subprocess.Popen(command, stdout=out_fp, stderr=err_fp).wait()

    out_fp.close()
    err_fp.close()

    if exit_code != 0:

        print(f"Command exited with {exitCode}.")
        print(command)
        print(f"Output written to {outputBasePath}.")

    return exit_code 


def compute_fiber_tract_measurements(
    in_fname,
    out_path,
    atlas_path,
    slicer_bin_path,
    fibertractmeasurements_module_path,
):

    # Apply white matter analysis
    print("WMA...")

    command = [
        "wm_apply_ORG_atlas_to_subject.sh",
	    "-i", f"{in_fname}",
	    "-o", f"{out_path}",
	    "-a", f"{atlas_path}",
	    "-s", f"{slicer_bin_path}",
	    "-d", "1",
	    "-m", f"{fibertractmeasurements_module_path}",
	    "-c", "2",
	    "-n", "4",
	]
    print(command)
    _ = run_command(command, out_path)

    print("Done.")


def main():

   #ScriptedLoadableModuleLogic.__init__()

   in_fname="/path/to/PQCed.vtk"
   out_path="/path/to/out"
   atlas_path="/path/to/org_atlas/ORG-Atlases-1.2"
   slicer_bin_path="/opt/Slicer-5.2.2-linux-amd64/Slicer"
   fibertractmeasurements_module_path="/opt/Slicer-5.2.2-linux-amd64/NA-MIC/Extensions-31382/SlicerDMRI/lib/Slicer-5.2/cli-modules/FiberTractMeasurements"

   compute_fiber_tract_measurements(
       in_fname,
       out_path,
       atlas_path,
       slicer_bin_path,
       fibertractmeasurements_module_path,
   )


if __name__ == "__main__":
    main()