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:
