This is a known bug. Please see
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
for a patch
On 10/14/2022 1:46 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
I receive an error when I try to run the sclimbic module, do you have
any suggestions on why this might be happening? : Loaded input image
from /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/GP1462~1/mri/nu.mgz
Traceback (most recent call last):
File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 1048, in <module>
main()
File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 232, in main
segmenter.process_files(**params)
File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 577, in process_files
post, seg, vox_counts, volumes, mean_probs = self.segment(image)
File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 497, in segment
conformed = self.preprocess(image)
File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 489, in preprocess
processed = image.conform(shape=(*self.inshape, self.nchannels),
voxsize=1.0, orientation='RAS', dtype='float32', copy=False)
File
"/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/image/framed.py",
line 574, in conform
conformed = conformed.reshape(shape, copy=False)
File
"/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/image/framed.py",
line 515, in reshape
delta = (np.array(shape) - np.array(self.baseshape)) / 2
ValueError: operands could not be broadcast together with shapes (4,)
(3,)
Segmentation fault
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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