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)
