# -*- coding: utf-8 -*- """ Created on Sat Dec 19 15:09:52 2015 @author: andric """ import os import sys import procs as pr if __name__ == '__main__': ss = int(sys.argv[1]) anat_dir = os.path.join(os.environ['avp'], 'nii', '%s_CNR.anat' % ss) fn_coef = os.path.join(anat_dir, 'T1_to_MNI_nonlin_coeff.nii.gz') in_fn = os.path.join(anat_dir, 'T1_subcort_seg.nii.gz') out_fn = os.path.join(anat_dir, '%s_T1_subcort_seg_fnirted_MNI2mm' % ss) logfile = os.path.join(anat_dir, 'applywarpFNIRT_T1_subcort_seg') pr.applywarpFNIRT(ss, in_fn, out_fn, fn_coef, 'nn', logfile)
import os import procs as pr if __name__ == '__main__': # subj_list = range(1, 19) subj_list = [1] for ss in subj_list: decon_dir = os.path.join(os.environ['avp'], 'nii', 'deconvolve_outs') vol_dir_pref = 'nii/%s_CNR.anat' % ss anat_dir = os.path.join(os.environ['avp'], vol_dir_pref) wholet1 = os.path.join(anat_dir, 'T1_biascorr.nii.gz') extrt1 = os.path.join(anat_dir, 'T1_biascorr_brain.nii.gz') premat = os.path.join(anat_dir, '%s_3.2mprage.mat' % ss) for i in range(1, 5): epi_pref = 'decon_out.mion.%d_%d.Powered.cleanEPI' % (ss, i) epi_nii_pref = os.path.join(decon_dir, epi_pref) pr.converttoNIFTI(decon_dir, '%s+orig' % epi_nii_pref, epi_nii_pref) in_fl = os.path.join(decon_dir, '%s.nii.gz' % epi_nii_pref) out_fl = os.path.join(decon_dir, '%s_flirted' % epi_nii_pref) pr.applywarpFLIRT(ss, decon_dir, in_fl, extrt1, out_fl, premat) fn_coef = os.path.join(anat_dir, 'T1_to_MNI_nonlin_coeff.nii.gz') in_fn = '%s.nii.gz' % out_fl out_fn = os.path.join(decon_dir, '%s_fnirted_MNI2mm' % epi_nii_pref) pr.applywarpFNIRT(ss, decon_dir, in_fn, out_fn, fn_coef)