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)
if __name__ == '__main__':
protocols = ['preference', 'mtt1', 'mtt2', 'tom', 'self']
protocols = ['retino']
protocols = [
'lyon1', 'lyon2', 'audio1', 'audio2', 'stanford1', 'stanford2',
'stanford3'
]
protocols = ['archi', 'screening', 'rsvp-language', 'hcp1', 'hcp2']
for protocol in protocols:
jobfile = 'ini_files/IBC_preproc_%s.ini' % protocol
acquisition = protocol # 'clips4' #
lowres = False
subject_session = sorted(get_subject_session(acquisition))
Parallel(n_jobs=4)(delayed(run_subject_surface_glm)(
jobfile, subject, session, protocol, lowres=lowres)
for (subject, session) in subject_session)
"""
import os
import nibabel as nib
import numpy as np
from ibc_public.utils_pipeline import fixed_effects_img, fixed_effects_surf
from pipeline import get_subject_session
from nilearn.plotting import plot_stat_map
from nilearn.image import math_img
# where to work and write
SMOOTH_DERIVATIVES = '/neurospin/ibc/smooth_derivatives'
DERIVATIVES = '/neurospin/ibc/derivatives'
THREE_MM = '/neurospin/ibc/3mm'
# misc info on preference protocol
subject_session = get_subject_session('preference')
categories = ['Faces', 'Food', 'Houses', 'Paintings']
categories_ = categories
contrasts = ['constant', 'linear', 'quadratic']
# mask image
_package_directory = os.path.dirname(os.path.abspath(__file__))
mask_img = os.path.join(_package_directory, '../ibc_data',
'gm_mask_1_5mm.nii.gz')
def compute_contrast(con_imgs, var_imgs, mask_img):
if isinstance(mask_img, str):
mask_img = nib.load(mask_img)
mask = mask_img.get_fdata().astype(np.bool)
print(
os.system(
'$FREESURFER_HOME/bin/mri_vol2surf --src %s --o %s '
'--out_type gii --srcreg %s --hemi rh --projfrac-avg 0 2 0.1'
% (fmri_session, right_fmri_tex, regheader)))
# resample to fsaverage
left_fsaverage_fmri_tex = os.path.join(
fs_dir, basename + '_fsaverage_lh.gii')
right_fsaverage_fmri_tex = os.path.join(
fs_dir, basename + '_fsaverage_rh.gii')
print(
os.system('$FREESURFER_HOME/bin/mri_surf2surf --srcsubject %s '
'--srcsurfval %s --trgsurfval %s --trgsubject ico '
'--trgicoorder 7 --hemi lh --nsmooth-out 5' %
(subject, left_fmri_tex, left_fsaverage_fmri_tex)))
print(
os.system('$FREESURFER_HOME/bin/mri_surf2surf --srcsubject %s '
'--srcsurfval %s --trgsubject ico --trgicoorder 7 '
'--trgsurfval %s --hemi rh --nsmooth-out 5' %
(subject, right_fmri_tex, right_fsaverage_fmri_tex)))
subject_sessions = sorted(get_subject_session('enumeration'))
Parallel(n_jobs=4)(delayed(project_volume)(
work_dir, subject_session[0], [subject_session[1]], do_bbr=True)
for subject_session in subject_sessions)
if len(subject['session_id']) > 0:
if protocol == 'clips4':
first_level(subject, compcorr=True, additional_regressors=RETINO_REG,
smooth=smooth, mask_img=mask_img)
else:
first_level(subject, compcorr=True, smooth=smooth, mask_img=mask_img)
fixed_effects_analysis(subject, mask_img=mask_img)
if __name__ == '__main__':
prepare_derivatives(IBC)
smooth = 5
for protocol in ['enumeration']: # ['hcp1', 'hcp2', 'rsvp-language', 'mtt2' 'preferences', 'tom']
jobfile = 'ini_files/IBC_preproc_%s.ini' % protocol
subject_session = get_subject_session(protocol)
subject_session = [('sub-01', 'ses-20'), ('sub-09', 'ses-18')]
Parallel(n_jobs=4)(
delayed(run_subject_glm)(jobfile, protocol, subject, session, smooth)
for (subject, session) in subject_session)
smooth = None
for protocol in ['enumeration']:
jobfile = 'ini_files/IBC_preproc_%s.ini' % protocol
Parallel(n_jobs=4)(
delayed(run_subject_glm)(jobfile, protocol, subject, session, smooth)
for (subject, session) in subject_session)
for protocol in ['enumeration']: # ['lyon1', 'preferences', 'screening', 'hcp1', 'hcp2', , 'mtt2' 'preferences', 'screening', 'rsvp-language', 'clips4' 'archi', ]
jobfile = 'ini_files/IBC_preproc_%s.ini' % protocol
# resample to fsaverage5
left_fsaverage_fmri_tex = os.path.join(
fs_dir, basename + '_fsaverage5_lh.gii')
right_fsaverage_fmri_tex = os.path.join(
fs_dir, basename + '_fsaverage5_rh.gii')
print(os.system(
'$FREESURFER_HOME/bin/mri_surf2surf --srcsubject %s '
'--srcsurfval %s --trgsurfval %s --trgsubject ico '
'--trgicoorder 5 --hemi lh --nsmooth-out 5' %
(subject, left_fmri_tex, left_fsaverage_fmri_tex)))
print(os.system(
'$FREESURFER_HOME/bin/mri_surf2surf --srcsubject %s '
'--srcsurfval %s --trgsubject ico --trgicoorder 5 '
'--trgsurfval %s --hemi rh --nsmooth-out 5' %
(subject, right_fmri_tex, right_fsaverage_fmri_tex)))
protocols = ['archi', 'screening', 'rsvp-language', 'hcp1', 'hcp2']
protocols = ['preference', 'mtt1', 'mtt2', 'clips4', 'tom', 'self']
protocols = ['clips1', 'clips2', 'clips3']
protocols = ['lyon1', 'lyon2', 'audio1', 'audio2', 'stanford1',
'stanford2', 'stanford3']
subject_sessions = sorted(get_subject_session(protocols))
Parallel(n_jobs=4)(
delayed(project_volume)(work_dir, subject_session[0], [subject_session[1]],
do_bbr=True)
for subject_session in subject_sessions)