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)