def execute(): #pylint: disable=unused-variable
lut_input_path = 'LUT.txt'
if not os.path.exists('LUT.txt'):
freesurfer_home = os.environ.get('FREESURFER_HOME', '')
if not freesurfer_home:
raise MRtrixError(
'Environment variable FREESURFER_HOME is not set; please run appropriate FreeSurfer configuration script, set this variable manually, or provide script with path to file FreeSurferColorLUT.txt using -lut option'
)
lut_input_path = os.path.join(freesurfer_home,
'FreeSurferColorLUT.txt')
if not os.path.isfile(lut_input_path):
raise MRtrixError(
'Could not find FreeSurfer lookup table file (expected location: '
+ lut_input_path + '), and none provided using -lut')
if app.ARGS.sgm_amyg_hipp:
lut_output_file_name = 'FreeSurfer2ACT_sgm_amyg_hipp.txt'
else:
lut_output_file_name = 'FreeSurfer2ACT.txt'
lut_output_path = os.path.join(path.shared_data_path(),
path.script_subdir_name(),
lut_output_file_name)
if not os.path.isfile(lut_output_path):
raise MRtrixError(
'Could not find lookup table file for converting FreeSurfer parcellation output to tissues (expected location: '
+ lut_output_path + ')')
# Initial conversion from FreeSurfer parcellation to five principal tissue types
run.command('labelconvert input.mif ' + lut_input_path + ' ' +
lut_output_path + ' indices.mif')
# Crop to reduce file size
if app.ARGS.nocrop:
image = 'indices.mif'
else:
image = 'indices_cropped.mif'
run.command(
'mrthreshold indices.mif - -abs 0.5 | mrgrid indices.mif crop ' +
image + ' -mask -')
# Convert into the 5TT format for ACT
run.command('mrcalc ' + image + ' 1 -eq cgm.mif')
run.command('mrcalc ' + image + ' 2 -eq sgm.mif')
run.command('mrcalc ' + image + ' 3 -eq wm.mif')
run.command('mrcalc ' + image + ' 4 -eq csf.mif')
run.command('mrcalc ' + image + ' 5 -eq path.mif')
run.command(
'mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - result.mif -datatype float32'
)
run.command('mrconvert result.mif ' + path.from_user(app.ARGS.output),
mrconvert_keyval=path.from_user(app.ARGS.input, False),
force=app.FORCE_OVERWRITE)
def get_inputs(): #pylint: disable=unused-variable
run.command('mrconvert ' + path.from_user(app.ARGS.input) + ' ' +
path.to_scratch('input.mif'))
if app.ARGS.lut:
run.function(shutil.copyfile, path.from_user(app.ARGS.lut, False),
path.to_scratch('LUT.txt', False))