def get_ras_using_sftp(args):
for subject in args.subject:
necessary_files = {'electrodes': ['{}_RAS.xlsx'.format(subject)]}
utils.prepare_subject_folder(necessary_files, subject,
args.remote_subject_dir, pu.SUBJECTS_DIR,
True, args.sftp_username,
args.sftp_domain)
def get_labels_data(subject, atlas):
necessary_files = {
'label': ['{}.{}.annot'.format(hemi, atlas) for hemi in utils.HEMIS]
}
remote_subject_dir = op.join(FS_ROOT,
'{0}_recon.long.{0}-base'.format(subject))
utils.prepare_subject_folder(necessary_files, subject, remote_subject_dir,
SUBJECTS_DIR)
def prepare_files(subject, remote_subjects_dir):
necessary_files = {
'mri': ['wm.mgz'],
'label': ['rh.cortex.label', 'lh.cortex.label'],
'surf': ['lh.thickness', 'rh.thickness']
}
utils.prepare_subject_folder(necessary_files, subject,
op.join(remote_subjects_dir, subject),
SUBJECTS_DIR)
def get_output_using_sftp(subjects, subject_to):
sftp_domain = 'door.nmr.mgh.harvard.edu'
sftp_username = '******'
remote_subject_dir = '/space/thibault/1/users/npeled/subjects/{subject}'
necessary_files = {
'mri_cvs_register_to_{}'.format(subject_to):
['combined_to{}_elreg_afteraseg-norm.tm3d'.format(subject_to)]
}
password = ''
for subject in subjects:
print('Getting tm3d file for {}'.format(subject))
utils.make_dir(op.join(SUBJECTS_DIR, subject, 'electrodes'))
ret, password_temp = utils.prepare_subject_folder(
necessary_files,
subject,
remote_subject_dir.format(subject=subject.lower()),
SUBJECTS_DIR,
True,
sftp_username,
sftp_domain,
sftp_password=password)
if not ret:
print('Error in copying the file!')
if password_temp != '':
password = password_temp
def prepare_files_for_subjects(subjects,
remote_subject_templates,
overwrite=False):
necessary_files = {
'surf': [
'lh.inflated', 'rh.inflated', 'lh.pial', 'rh.pial', 'rh.white',
'lh.white', 'lh.smoothwm', 'rh.smoothwm', 'rh.sulc', 'lh.sulc',
'lh.sphere', 'rh.sphere', 'lh.inflated.K', 'rh.inflated.K',
'lh.inflated.H', 'rh.inflated.H'
],
'label': ['lh.aparc.annot', 'rh.aparc.annot']
}
# subjects = pu.decode_subjects(['MG*'], remote_subject_template)
good_subjects = []
for subject in subjects:
for remote_subject_template in remote_subject_templates:
remote_subject_dir = utils.build_remote_subject_dir(
remote_subject_template, subject)
all_files_exist = utils.prepare_subject_folder(
necessary_files,
subject,
remote_subject_dir,
SUBJECTS_DIR,
overwrite_files=overwrite,
print_missing_files=False)
if all_files_exist:
good_subjects.append(subject)
break
return good_subjects
def get_subject_files(subject, necessary_files, remote_subject_dir):
if not op.isdir(remote_subject_dir):
return False
return utils.prepare_subject_folder(necessary_files,
subject,
remote_subject_dir,
SUBJECTS_DIR,
print_traceback=False)
def prepare_files_for_subjects(subjects,
remote_subject_templates,
sftp=False,
sftp_username='',
sftp_domain='',
overwrite=False):
necessary_files = {
'surf': [
'lh.inflated', 'rh.inflated', 'lh.pial', 'rh.pial', 'rh.white',
'lh.white', 'lh.smoothwm', 'rh.smoothwm', 'rh.sulc', 'lh.sulc',
'lh.sphere', 'rh.sphere', 'lh.inflated.K', 'rh.inflated.K',
'lh.inflated.H', 'rh.inflated.H'
],
'mri': [
'aseg.mgz', 'norm.mgz', 'ribbon.mgz', 'T1.mgz', 'orig.mgz',
'brain.mgz'
],
'label': ['lh.aparc.annot', 'rh.aparc.annot']
}
# subjects = pu.decode_subjects(['MG*'], remote_subject_template)
good_subjects = []
for subject in subjects:
for remote_subject_template in remote_subject_templates:
remote_subject_template = remote_subject_template.replace(
'{hosp}', subject[:2])
remote_subject_dir = utils.build_remote_subject_dir(
remote_subject_template, subject)
all_files_exist, _ = utils.prepare_subject_folder(
necessary_files,
subject,
remote_subject_dir,
SUBJECTS_DIR,
overwrite_files=overwrite,
sftp=sftp,
sftp_username=sftp_username,
sftp_domain=sftp_domain,
print_missing_files=False)
if all_files_exist:
good_subjects.append(subject)
break
bad_subjects = list(set(subjects) - set(good_subjects))
print('prepare_files: {}/{} good subjects'.format(len(good_subjects),
len(subjects)))
print('Good: {}'.format(good_subjects))
print('Bad: {}'.format(bad_subjects))
# if len(bad_subjects) > 0:
# from src.preproc import anatomy as anat
# for subject in bad_subjects:
# args = anat.read_cmd_args(dict(
# subject=subject,
# remote_subject_dir='/mnt/cashlab/Original Data/MG/{subject}/{subject}_Notes_and_Images/{subject}_SurferOutput',
# function='prepare_subject_folder'
# ))
# args.necessary_files = necessary_files
# pu.run_on_subjects(args, anat.main)
return good_subjects
def prepare_subject_folder(subject,
remote_subject_dir,
args,
necessary_files=None):
if necessary_files is None:
necessary_files = args.necessary_files
return utils.prepare_subject_folder(necessary_files, subject,
remote_subject_dir, SUBJECTS_DIR,
args.sftp, args.sftp_username,
args.sftp_domain, args.sftp_password,
args.overwrite_fs_files,
args.print_traceback, args.sftp_port)
def preproc_anat(subjects, overwrite_files=False):
good_subjects = []
for subject in subjects:
# utils.make_dir(op.join(MMVT_DIR, subject, 'fmri'))
# utils.make_dir(op.join(MMVT_DIR, '{}_rescan'.format(subject), 'fmri'))
scan_ret = utils.prepare_subject_folder(
anat.get_necessary_files(),
subject,
op.join(FS_ROOT, '{0}_recon.long.{0}-base'.format(subject)),
SUBJECTS_DIR,
overwrite_files=overwrite_files)[0]
rescan_ret = utils.prepare_subject_folder(
anat.get_necessary_files(),
'{}_rescan'.format(subject),
op.join(FS_ROOT, '{0}_B_recon.long.{0}-base'.format(subject)),
SUBJECTS_DIR,
overwrite_files=overwrite_files)[0]
if scan_ret and rescan_ret:
good_subjects.append(subject)
print('{}/{} good subjects'.format(len(good_subjects), len(subjects)))
return good_subjects
