def run_subject_glm(jobfile, protocol, subject, session=None, smooth=None,
lowres=False):
""" Create jobfile and run it """
if protocol == 'preferences' and subject in ['sub-11']:
jobfile = 'ini_files/IBC_preproc_preferences_sub-11.ini'
output_name = os.path.join(
'/tmp', os.path.basename(jobfile)[:-4] + '_%s.ini' % subject)
_adapt_jobfile(jobfile, subject, output_name, session)
list_subjects_update = generate_glm_input(output_name, smooth, lowres)
clean_anatomical_images(IBC)
if lowres:
mask_img = '../ibc_data/gm_mask_3mm.nii.gz'
else:
mask_img = '../ibc_data/gm_mask_1_5mm.nii.gz'
for subject in list_subjects_update:
subject['onset'] = [onset for onset in subject['onset']
if onset is not None]
clean_subject(subject)
if len(subject['session_id']) > 0:
if protocol == 'clips4':
first_level(subject, compcorr=True,
additional_regressors=RETINO_REG,
smooth=smooth, mask_img=mask_img)
else:
first_level(subject, compcorr=True, smooth=smooth,
mask_img=mask_img)
fixed_effects_analysis(subject, mask_img=mask_img)
def run_subject_surface_glm(jobfile, subject, session, protocol, lowres=False):
""" Create jobfile and run it """
output_name = os.path.join(
'/tmp',
os.path.basename(jobfile)[:-4] + '_%s.ini' % subject)
_adapt_jobfile(jobfile, subject, output_name, session)
list_subjects_update = generate_glm_input(output_name, lowres)
clean_anatomical_images(IBC)
for subject in list_subjects_update:
clean_subject(subject)
if len(subject['session_id']) > 0:
print(len(subject['session_id']))
if len(subject['session_id']) > 0:
#if protocol == 'retino':
# first_level(subject, compcorr=True,
# additional_regressors=RETINO_REG,
# smooth=None, surface=True)
#else:
first_level(subject, compcorr=True, smooth=None, surface=True)
fixed_effects_analysis(subject, surface=True, lowres=True)