for subject_label in subjects_to_analyze:
label = 'sub-' + subject_label
print('running pre-processing for ' + label)
# Read DWI in BIDS derivatives folder
all_dwi_images = glob.glob(
os.path.join(app.args.in_dir, label, '*dwi', '*_dwi.nii*'))
# Create output subject directory
subject_dir = os.path.join(all_subjects_dir, subject_label)
if not os.path.exists(subject_dir):
os.mkdir(subject_dir)
# Check existence output files from this analysis level
dwi_preproc_file = os.path.join(subject_dir, 'dwi_preproc.mif')
app.checkOutputPath(dwi_preproc_file)
dwi_bias_file = os.path.join(subject_dir, 'dwi_preproc_bias.mif')
app.checkOutputPath(dwi_bias_file)
output_mask = os.path.join(subject_dir, 'mask.mif')
app.checkOutputPath(output_mask)
# DW gradient files
grad_prefix = os.path.join(app.args.in_dir, label, 'dwi',
label + '_dwi')
if not (os.path.isfile(grad_prefix + '.bval')
and os.path.isfile(grad_prefix + '.bvec')):
grad_prefix = os.path.join(app.args.in_dir, 'dwi')
if not (os.path.isfile(grad_prefix + '.bval')
and os.path.isfile(grad_prefix + '.bvec')):
app.error('Unable to locate valid diffusion gradient table')
grad_import_option = ' -fslgrad ' + grad_prefix + '.bvec ' + grad_prefix + '.bval'
def checkOutputPaths(): #pylint: disable=unused-variable
from mrtrix3 import app
app.checkOutputPath(app.args.output)
def checkOutputPaths():
from mrtrix3 import app
app.checkOutputPath(app.args.output)
def checkOutputPaths(): #pylint: disable=unused-variable from mrtrix3 import app app.checkOutputPath(app.args.output)
def checkOutputPaths(): from mrtrix3 import app app.checkOutputPath(app.args.output)
def checkOutputPaths(): from mrtrix3 import app app.checkOutputPath(app.args.out_sfwm) app.checkOutputPath(app.args.out_gm) app.checkOutputPath(app.args.out_csf)
def checkOutputPaths():
from mrtrix3 import app
app.checkOutputPath(app.args.out_sfwm)
app.checkOutputPath(app.args.out_gm)
app.checkOutputPath(app.args.out_csf)