def align_funcs(funcs, logger): allmove = [] allmoved = [funcs[0]] func_target = funcs[0] for movin in funcs[1:]: tmpaff = reg.affine_register_cc(func_target, movin) if tmpaff is None: continue displacement, translate, angles = xfm.params_from_ants(tmpaff) allmove.append([translate.tolist() + angles + [displacement]]) moved = reg.apply_transform(movin, tmpaff, target = func_target) allmoved.append(moved) return allmove, allmoved
reg.function_logger(rootdir)
logger = logging.getLogger('antsregister.wrapper')
for datadir in allseries:
logger.info(datadir)
globstr = os.path.join(datadir, 'B13-005_sess*.nii.gz')
allf = sorted(glob(globstr))
target = allf[0]
basedir, _ = os.path.split(target)
reg.function_logger(basedir)
allmove = []
allmoved = [target]
for movin in allf[1:3]:
tmpaff = reg.affine_register_cc(target, movin)
if tmpaff is None:
continue
displacement, translate, angles = xfm.params_from_ants(tmpaff)
allmove.append([translate.tolist() + angles + [displacement]])
moved = reg.apply_affine(movin, tmpaff)
allmoved.append(moved)
## merge aligned into 4D
merged_fname = os.path.join(datadir, 'aligned_4d.nii.gz')
try:
merged_img = ni.concat_images(allmoved)
merged_img.to_filename(merged_fname)
except:
cmd = 'fslmerge -t %s '%(merged_fname)
cmd = cmd + ' '.join([x for x in allmoved])
os.system(cmd)
allmove = np.asarray(allmove).squeeze()
dims = ('x','y','z')
cols = ['trans_%s'%x for x in dims] + ['rot_%s'%x for x in dims] +\
