    def full_warp_recon(self):

        T1_orig_file = os.path.join(self.subj_dir, self.subj, 'acpc', 'T1_orig.nii')

        MRCTwarp_output_dir = os.path.join(self.img_pipe_dir,'MRCTwarpout')

        os.mkdir(MRCTwarp_output_dir)

        preCT_file = os.path.join(self.subj_dir, self.subj, 'CT', 'preCT.nii')

        postCT_file = os.path.join(self.subj_dir, self.subf, 'CT', 'postCT.nii')

        MRCTwarp = os.path.join(self.img_pipe_dir, 'SupplementalScripts', 'call_matlabwarp.sh')

        os.system('%s %s %s %s' %(MRCTwarp, preCT_file, postCT_file, T1_orig_file))

        CT_final_aligned = os.path.join(MRCTwarp_output_dir, 'cpostrigid/result.0.nii.gz')

        MR_final_aligned = os.path.join(MRCTwarp_output_dir, 'mcrigid/result.0.nii.gz')

        MR_final_warp = os.path.join(MRCTwarp_output_dir, 'mcnonrigid/result.nii')

        reg_CT = os.path.join(self.img_pipe_dir,'CT/rCT.nii')

        os.system('cp %s %s' %(CT_final_aligned, CT_dir))

        self.prep_recon()

        readyforreconflag = os.path.join(self.img_pipe_dir,'tmp','readyforrecon')

        os.system('touch %s' %(readyforreconflag))