data_dir = '/scr/kennedy2/data_fbeyer/real/'+subject+'/' data_dir_WDR = '/scr/kennedy2/data_fbeyer/BIPS/WDR/Lemon_mod/'+subject+'/' #os.makedirs(data_dir) ##change this depending on location of freesurfer files freesurfer_dir = '/scr/kennedy2/LIFE/freesurfer_all/' resting_dir = '/scr/kennedy2/data_fbeyer/redo_subjects/'+subject+'/preprocessed/mod/resting/' standard_brain = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz' standard_brain_resampled = '/home/raid1/fbeyer/Documents/Scripts/RS-analysis/MNI/MNI_resampled.nii' standard_brain_mask = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain_mask.nii.gz' standard_brain_mask_resampled='/home/raid1/fbeyer/Documents/Scripts/RS-analysis/MNI/MNI_resampled_brain_mask.nii.gz' echo_space=0.000512 #in sec te_diff=2.46 #in ms epi_resolution = 3.0 TR=2.0 highpass=0.01 lowpass=0.1 vol_to_remove = 5 pe_dir = 'y-' fwhm_smoothing = 6.0 create_lemon_resting(subject=subject, working_dir=working_dir, data_dir=data_dir, data_dir_WDR=data_dir_WDR, freesurfer_dir=freesurfer_dir, out_dir=resting_dir, vol_to_remove=vol_to_remove, TR=TR, epi_resolution=epi_resolution, highpass=highpass, lowpass=lowpass,echo_space=echo_space, te_diff=te_diff,pe_dir=pe_dir,standard_brain = standard_brain, standard_brain_resampled = standard_brain_resampled, standard_brain_mask = standard_brain_mask, standard_brain_mask_resampled = standard_brain_mask_resampled, fwhm_smoothing = fwhm_smoothing)
mode=sys.argv[1] if mode == 's': subjects=[sys.argv[2]] elif mode == 'f': with open(sys.argv[2], 'r') as f: subjects = [line.strip() for line in f] for subject in subjects: print 'Running subject '+subject working_dir = '/scr/ilz2/LEMON_LSD/working_dir_lemon/'+subject+'/' data_dir = '/scr/ilz2/LEMON_LSD/'+subject+'/' freesurfer_dir = '/scr/ilz2/LEMON_LSD/freesurfer/' lemon_dir = '/scr/ilz2/LEMON_LSD/'+subject+'/preprocessed/lemon_resting/' echo_space=0.00067 #in sec te_diff=2.46 #in ms epi_resolution = 2.3 TR=1.4 highpass=0.01 lowpass=0.1 vol_to_remove = 5 pe_dir = 'y-' create_lemon_resting(subject=subject, working_dir=working_dir, data_dir=data_dir, freesurfer_dir=freesurfer_dir, out_dir=lemon_dir, vol_to_remove=vol_to_remove, TR=TR, epi_resolution=epi_resolution, highpass=highpass, lowpass=lowpass,echo_space=echo_space, te_diff=te_diff, pe_dir=pe_dir)
standard_brain_mask_resampled = '/home/raid1/fbeyer/Documents/Scripts/RS-analysis/MNI/MNI_resampled_brain_mask.nii.gz' echo_space = 0.000512 #in sec te_diff = 2.46 #in ms epi_resolution = 3.0 TR = 2.0 highpass = 0.01 lowpass = 0.1 vol_to_remove = 5 pe_dir = 'y-' fwhm_smoothing = 6.0 create_lemon_resting( subject=subject, working_dir=working_dir, data_dir=data_dir, freesurfer_dir=freesurfer_dir, out_dir=resting_dir, vol_to_remove=vol_to_remove, TR=TR, epi_resolution=epi_resolution, highpass=highpass, lowpass=lowpass, echo_space=echo_space, te_diff=te_diff, pe_dir=pe_dir, standard_brain=standard_brain, standard_brain_resampled=standard_brain_resampled, standard_brain_mask=standard_brain_mask, standard_brain_mask_resampled=standard_brain_mask_resampled, fwhm_smoothing=fwhm_smoothing)
for subject in subjects: print 'Running subject ' + subject working_dir = '/scr/ilz2/LEMON_LSD/working_dir_lemon/' + subject + '/' data_dir = '/scr/ilz2/LEMON_LSD/' + subject + '/' freesurfer_dir = '/scr/ilz2/LEMON_LSD/freesurfer/' lemon_dir = '/scr/ilz2/LEMON_LSD/' + subject + '/preprocessed/lemon_resting/' echo_space = 0.00067 #in sec te_diff = 2.46 #in ms epi_resolution = 2.3 TR = 1.4 highpass = 0.01 lowpass = 0.1 vol_to_remove = 5 pe_dir = 'y-' create_lemon_resting(subject=subject, working_dir=working_dir, data_dir=data_dir, freesurfer_dir=freesurfer_dir, out_dir=lemon_dir, vol_to_remove=vol_to_remove, TR=TR, epi_resolution=epi_resolution, highpass=highpass, lowpass=lowpass, echo_space=echo_space, te_diff=te_diff, pe_dir=pe_dir)