def calc_labels_avg(target_subject, hemi, atlas, fmri_fname, res_dir, cwd, overwrite=True, output_txt_fname='',
output_sum_fname='', ret_files_name=False, **kargs):
def get_labels_names(line):
label_name = line.split()[4]
label_nums = utils.find_num_in_str(label_name)
label_num = label_nums[-1] if len(label_nums) > 0 else ''
if label_num != '':
name_len = label_name.find('_{}'.format(label_num)) + len(str(label_num)) + 1
label_name = '{}-{}'.format(label_name[:name_len], hemi)
return label_name
if output_txt_fname == '':
output_txt_fname = op.join(res_dir, '{}_{}_{}.txt'.format(utils.namebase(fmri_fname), atlas, hemi))
if output_sum_fname == '':
output_sum_fname = op.join(res_dir, '{}_{}_{}.sum'.format(utils.namebase(fmri_fname), atlas, hemi))
if not op.isfile(output_txt_fname) or not op.isfile(output_sum_fname) or overwrite:
print('Running mri_segstats on {} ({})'.format(fmri_fname, utils.file_modification_time(fmri_fname)))
utils.partial_run_script(locals(), cwd=cwd)(mri_segstats)
if not op.isfile(output_txt_fname):
raise Exception('The output file was not created!')
labels_data = np.genfromtxt(output_txt_fname).T
labels_names = utils.read_list_from_file(output_sum_fname, get_labels_names, 'rb')
if ret_files_name:
return labels_data, labels_names, output_txt_fname, output_sum_fname
else:
return labels_data, labels_names
def find_good_subjects_indices(all_subjects):
good_subjects = utils.read_list_from_file(
op.join(root_path, 'good_subjects.txt'))
return [
ind for ind in range(len(all_subjects))
if all_subjects[ind] in good_subjects
]
def decode_subjects(subjects):
for sub in subjects:
if '*' in sub:
subjects.remove(sub)
subjects.extend([
utils.namebase(fol)
for fol in glob.glob(op.join(SUBJECTS_DIR, sub))
])
elif 'file:' in sub:
subjects.remove(sub)
subjects.extend(utils.read_list_from_file(sub[len('file:'):]))
return subjects
def decode_subjects(subjects, remote_subject_dir=''):
for sub in subjects:
if '*' in sub:
subjects.remove(sub)
subjects.extend([
utils.namebase(fol)
for fol in glob.glob(op.join(SUBJECTS_DIR, sub))
])
if remote_subject_dir != '':
for fol in glob.glob(
op.join(remote_subject_dir.format(subject=sub))):
start_ind = utils.namebase(remote_subject_dir).index(
'{subject}')
end_ind = re.search(
'[-_,\.!?]',
utils.namebase(fol)[start_ind:]).start() + start_ind
subjects.append(utils.namebase(fol)[start_ind:end_ind])
subjects = list(set(subjects))
elif 'file:' in sub:
subjects.remove(sub)
subjects.extend(utils.read_list_from_file(sub[len('file:'):]))
return subjects