diff --git a/cortex/dataset/braindata.py b/cortex/dataset/braindata.py index a04b1ba3..6be206e7 100644 --- a/cortex/dataset/braindata.py +++ b/cortex/dataset/braindata.py @@ -1,10 +1,12 @@ import hashlib from copy import deepcopy -import numpy as np + import h5py +import numpy as np from ..database import db + class BrainData(object): """ Abstract base class for brain data. @@ -592,9 +594,10 @@ def blend_curvature(self, alpha, threshold=0, brightness=0.5, def _find_mask(nvox, subject, xfmname): + import glob import os import re - import glob + import nibabel files = db.get_paths(subject)['masks'].format(xfmname=xfmname, type="*") for fname in glob.glob(files): @@ -602,7 +605,7 @@ def _find_mask(nvox, subject, xfmname): mask = nib.get_fdata().T != 0 if nvox == np.sum(mask): fname = os.path.split(fname)[1] - name = re.compile(r'mask_([\w]+).nii.gz').search(fname) + name = re.compile(r'mask_(.+).nii.gz').search(fname) return name.group(1), mask raise ValueError('Cannot find a valid mask')