[Neuroimaging] Python stuck when loading an overlay

Chuanji Gao chuanjigao at gmail.com
Mon Feb 28 11:36:19 EST 2022


Hi,

I'm running PySurfer using Spyder on my Mac Big Sur.
Though I had no issue of loading one image, my Spyder would be
not responding everytime I'm loading an overlay (see attached).
Can someone give me some advice?

Here is the code I used:

import os
from surfer import Brain
subject_id = "fsaverage"
hemi = "lh"
surf = "inflated"
print(subject_id)
os.environ["SUBJECTS_DIR"] = "/Applications/freesurfer/7.1.1/subjects"
brain = Brain(subject_id, hemi, surf, background="white")
overlay_file = "/Volumes/T7/example/spmT_0008.nii"
brain.add_overlay(overlay_file)

Best,
Chuanji
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