# -*- 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)