[tract, '_mask.nii.gz'])
if len(tract_mask) > 1:
logging.error(
'More than one mask file found for tract: {}'.format(
tract))
logging.error('Files found: {}'.format(tract_mask))
raise RuntimeError('Found more than one mask file!')
#find_masks() returns a list, even if there is only one file found
tract_mask = tract_mask[0]
include_roi_list = eda.find_masks(tract_mask_dir,
[tract, '_include.nii.gz'])
#Transform mask and spheres into subject space
subspace_mask = eda.transform_roi(in_image=tract_mask,
add_suffix=sub,
ref=input_dti,
transform=transform_file)
if subspace_mask is None:
logging.error(
'Transforming mask to subject space failed: {}'.format(
in_mask))
raise RuntimeError(
'Transforming mask to subject space failed!')
#Move the transformed mask to the subject's directory
shutil.move(subspace_mask, sub_output_dir)
#Move the aligned mask to the subject's directory
subspace_include_roi_list = []
for element in include_roi_list:
out_name = eda.transform_roi(in_image=element,
for tract in tract_list:
try:
#Set up mask and sphere file names
tract_mask = os.path.join(tract_mask_dir, tract_mask_temp.format(tract=tract))
tract_spheres = os.path.join(tract_mask_dir, tract_sphere_temp.format(tract=tract))
#Set up subject-space mask and sphere file names
sub_tract_mask = os.path.join(sub_output_dir, sub_tract_mask_temp.format(tract=tract, sub=sub))
sub_sphere_mask = os.path.join(sub_output_dir, sub_tract_spheres_temp.format(tract=tract, sub=sub))
tckgen_out = os.path.join(sub_output_dir, tckgen_out_temp.format(sub=sub, ses=ses, run=run, tract=tract))
#Transform mask and spheres into subject space
if not os.path.exists(sub_tract_mask):
okay = eda.transform_roi(in_image=tract_mask, out_image=sub_tract_mask, ref=ref_image, transform=transform_file)
if okay is None:
logging.error('Transforming tract mask to subject space failed!')
raise RuntimeError('Transforming tract mask to subject space failed!')
else:
logging.info('Subject tract mask already exists: {}'.format(sub_tract_mask))
if not os.path.exists(sub_sphere_mask):
okay = eda.transform_roi(in_image=tract_spheres, out_image=sub_sphere_mask, ref=ref_image, transform=transform_file)
if okay is None:
logging.error('Transforming sphere mask to subject space failed!')
raise RuntimeError('Transforming sphere mask to subject space failed!')
else:
logging.info('Subject sphere mask already exists: {}'.format(sub_sphere_mask))
#Run tckgen to generate tracks