output_dict[sub][cope] = {}
cope_dir = os.path.join(input_dir.format(sub=sub),
'cope{}.feat'.format(cope_labels[cope]))
output_dict[sub][cope]['dir'] = cope_dir
for roi in roi_list:
output_dict[sub][cope][roi] = {}
output_dir = os.path.join(cope_dir,
feat_output_dir.format(roi=roi))
roi_file = os.path.join(roi_dir,
'ROI_{roi}_final.nii.gz'.format(roi=roi))
if os.path.exists(output_dir):
print('Output directory already there; DELETING it!')
shutil.rmtree(output_dir)
#Run featquery on the intensity-masked ROI
report_file = eral.run_featquery(
cope_dir=cope_dir,
output_dir=feat_output_dir.format(roi=roi),
roi_file=roi_file)
# peak_file = os.path.join(cope_dir, feat_output_dir.format(roi=roi), 'peak_coords.txt')
if report_file is not None:
with open(report_file) as fid:
contents = fid.read()
else:
raise RuntimeError
output_dict[sub][cope][roi]['mean'] = contents.split()[5]
output_dict[sub][cope][roi]['stdev'] = contents.split()[9]
output_dict[sub][cope][roi]['max'] = contents.split()[8]
output_dict[sub][cope][roi]['max_x'] = contents.split()[10]
output_dict[sub][cope][roi]['max_y'] = contents.split()[11]
output_dict[sub][cope][roi]['max_z'] = contents.split()[12]
output_dict[sub][cope][roi]['max_xmm'] = contents.split()[13]
output_dict[sub][cope][roi]['max_ymm'] = contents.split()[14]
print('Running Sub: {}'.format(sub))
for cope in cope_labels:
print('Contrast: {}'.format(cope))
output_dict[sub][cope] = {}
cope_dir = os.path.join(input_dir.format(sub=sub,ses=ses), 'cope{}.feat'.format(cope_labels[cope]))
output_dict[sub][cope]['dir'] = cope_dir
for roi in roi_list:
output_dict[sub][cope][roi] = {}
output_dir = os.path.join(cope_dir, feat_output_dir.format(roi=roi))
roi_file = os.path.join(roi_dir.format(sub=sub), 'sub_{sub}_ROI_{roi}_final.nii.gz'.format(sub=sub,roi=roi))
if os.path.exists(output_dir):
print('Output directory already there; DELETING it!')
shutil.rmtree(output_dir)
#Run featquery on the intensity-masked ROI
report_file = eral.run_featquery(cope_dir=cope_dir, output_dir=feat_output_dir.format(roi=roi), roi_file=roi_file)
peak_file = os.path.join(cope_dir, feat_output_dir.format(roi=roi), 'peak_coords.txt')
if report_file is not None:
with open(report_file) as fid:
contents = fid.read()
else:
raise RuntimeError
output_dict[sub][cope][roi]['mean'] = contents.split()[5]
output_dict[sub][cope][roi]['stdev'] = contents.split()[9]
output_dict[sub][cope][roi]['max'] = contents.split()[8]
output_dict[sub][cope][roi]['max_x'] = contents.split()[10]
output_dict[sub][cope][roi]['max_y'] = contents.split()[11]
output_dict[sub][cope][roi]['max_z'] = contents.split()[12]
output_dict[sub][cope][roi]['max_xmm'] = contents.split()[13]
output_dict[sub][cope][roi]['max_ymm'] = contents.split()[14]
output_dict[sub][cope][roi]['max_zmm'] = contents.split()[15]