shutil.rmtree(coregdir) continue cbrainmask = bg.copy_file(brainmask, coregdir) cbrainmask = bg.unzip_file(cbrainmask) # aparc aseg globstr = os.path.join(basedir, 'anatomy', '*aparc_aseg.nii*') aparc = pp.find_single_file(globstr) if aparc is None: logging.error('%s not found. skipping' % globstr) shutil.rmtree(coregdir) continue caparc = bg.copy_file(aparc, coregdir) caparc = bg.unzip_file(caparc) # cerebellum globstr = os.path.join(pth, 'ref_region', 'grey_cerebellum.nii*') cere = pp.find_single_file(globstr) if cere is None: logging.error('%s not found. skipping' % globstr) shutil.rmtree(coregdir) continue ccere = bg.copy_file(cere, coregdir) ccere = bg.unzip_file(ccere) # have all out files, coreg xfm = os.path.join(coregdir, 'mri_to_pet.mat') corgout = pp.invert_coreg(cbrainmask, mean_20min, xfm) pp.reslice(mean_20min, cbrainmask) pp.apply_transform_onefile(xfm, ccere) pp.reslice(mean_20min, ccere) pp.apply_transform_onefile(xfm, caparc) pp.reslice(mean_20min, caparc)
# find PET pet = movedmean # use previously made summed image # copy files to tmp dir logging.info("coreg ref region to %s" % pet) coreg_dir, exists = bg.make_dir(tracerdir, dirname="coreg_mri2fdg") if exists: logging.warning("existing dir %s remove to re-run" % (coreg_dir)) continue cmri = bg.copy_file(mri, coreg_dir) cpons = bg.copy_file(pons, coreg_dir) cpet = bg.copy_file(pet, coreg_dir) caparc = bg.copy_file(aparc, coreg_dir) xfm_file = pp.make_transform_name(cpet, cmri) logging.info("coreg %s" % (subid)) corg_out = pp.invert_coreg(cmri, cpet, xfm_file) if not corg_out.runtime.returncode == 0: logging.warning(corg_out.runtime.stderr) continue apply_out = pp.apply_transform_onefile(xfm_file, cpons) if not apply_out.runtime.returncode == 0: logging.warning(apply_out.runtime.stderr) continue apply_out = pp.apply_transform_onefile(xfm_file, caparc) if not apply_out.runtime.returncode == 0: logging.warning(apply_out.runtime.stderr) continue rout_mri = pp.reslice(cpet, cmri) if not rout_mri.runtime.returncode == 0: logging.warning(rout_mri.runtime.stderr) else:
cbrainmask = bg.unzip_file(cbrainmask) # aparc aseg globstr = os.path.join(basedir, 'anatomy', '*aparc_aseg.nii*') aparc = pp.find_single_file(globstr) if aparc is None: logging.error('%s not found. skipping'%globstr) shutil.rmtree(coregdir) continue caparc = bg.copy_file(aparc, coregdir) caparc = bg.unzip_file(caparc) # cerebellum globstr = os.path.join(pth, 'ref_region', 'grey_cerebellum.nii*') cere = pp.find_single_file(globstr) if cere is None: logging.error('%s not found. skipping'%globstr) shutil.rmtree(coregdir) continue ccere = bg.copy_file(cere, coregdir) ccere = bg.unzip_file(ccere) # have all out files, coreg xfm = os.path.join(coregdir, 'mri_to_pet.mat') corgout = pp.invert_coreg(cbrainmask, mean_20min,xfm) pp.reslice(mean_20min, cbrainmask) pp.apply_transform_onefile(xfm, ccere) pp.reslice(mean_20min, ccere) pp.apply_transform_onefile(xfm, caparc) pp.reslice(mean_20min, caparc)
# find PET pet = movedmean # use previously made summed image # copy files to tmp dir logging.info('coreg ref region to %s' % pet) coreg_dir, exists = bg.make_dir(tracerdir, dirname='coreg_mri2fdg') if exists: logging.warning('existing dir %s remove to re-run' % (coreg_dir)) continue cmri = bg.copy_file(mri, coreg_dir) cpons = bg.copy_file(pons, coreg_dir) cpet = bg.copy_file(pet, coreg_dir) caparc = bg.copy_file(aparc, coreg_dir) xfm_file = pp.make_transform_name(cpet, cmri) logging.info('coreg %s' % (subid)) corg_out = pp.invert_coreg(cmri, cpet, xfm_file) if not corg_out.runtime.returncode == 0: logging.warning(corg_out.runtime.stderr) continue apply_out = pp.apply_transform_onefile(xfm_file, cpons) if not apply_out.runtime.returncode == 0: logging.warning(apply_out.runtime.stderr) continue apply_out = pp.apply_transform_onefile(xfm_file, caparc) if not apply_out.runtime.returncode == 0: logging.warning(apply_out.runtime.stderr) continue rout_mri = pp.reslice(cpet, cmri) if not rout_mri.runtime.returncode == 0: logging.warning(rout_mri.runtime.stderr) else: