def process_subject(subdir, despike=False, spm=False):
_, sid = os.path.split(subdir)
rawdir = os.path.join(subdir, 'raw')
rlgndir, coregdir = find_make_workdir(subdir, despike, spm)
logger = setup_logging(coregdir, sid)
globtype = utils.defaults['aligned'].format(sid)
aligned = get_file(rlgndir, globtype)
bmask = get_file(rawdir, utils.defaults['anat_glob'])
aparc = get_file(rawdir, utils.defaults['aparc_glob'])
# copy files to coregdir
bmask = copy_file(bmask, coregdir)
aparc = copy_file(aparc, coregdir)
## mask brainmask with aparc
#bmask = utils.simple_mask(bmask, aparc, bmask)
## make mean
mean_aligned = os.path.join(coregdir,
'{0}_meanaligned.nii.gz'.format(sid))
mean_aligned = utils.mean_from4d(aligned, mean_aligned)
logger.info(mean_aligned)
## remove small values from mean (helps bias correction etc)
mean_aligned = utils.simple_mask(mean_aligned,
mean_aligned, mean_aligned, thr=100)
logger.info('thr meanaligned by {}'.format(100))
## register mean to bmask
xfm = reg.affine_register_mi(bmask, mean_aligned)
## invert and apply to brainmask and aparc
if xfm is None:
logger.error('ERROR: {0}: meanepi -> anat failed'.format(sid))
raise IOError('{0}: meanepi -> anat failed'.format(sid))
transform = '-i {0}'.format(xfm)
logger.info(transform)
rbmask = reg.apply_transform(bmask, transform, target=mean_aligned)
raparc = reg.apply_transform(aparc, transform,
target=mean_aligned, use_nn=True)
## make masks
wm_labels = utils.defaults['wm_labels']
vent_labels = utils.defaults['vent_labels']
wm_maskf = os.path.join(coregdir, '{0}_WM_mask.nii.gz'.format(sid))
wm_mask = utils.aparc_mask(raparc, wm_labels, wm_maskf)
vent_maskf = os.path.join(coregdir, '{0}_VENT_mask.nii.gz'.format(sid))
vent_mask = utils.aparc_mask(raparc, vent_labels, vent_maskf)
eroded_wm = utils.erode(wm_mask)
eroded_vent = utils.erode(vent_mask)
logger.info(vent_mask)
logger.info(eroded_vent)
logger.info(wm_mask)
logger.info(eroded_wm)
def make_realign(funcs):
""" uses ANTS to realign files"""
target = funcs[0]
aligned = [target]
xfms = []
for moving in funcs[1:]:
xfm = reg.affine_register_cc(target, moving)
if xfm is None:
raise IOError("{0} :affine register failed".format(moving))
xfms.append(xfm)
transformed = reg.apply_transform(moving, xfm, target=target)
if transformed is None:
raise IOError("{0}: apply xfm failed".format(moving))
aligned.append(transformed)
movement_array = transform.collate_affines(xfms)
return aligned, movement_array