External Email - Use Caution Dear FreeSurfer Developers, We are interested in implementing " mri_sclimbic_seg " from FreeSurfer 7.3.2 and are having trouble getting it to finish processing. When I tried to runmri_sclimbic_seg. I keep getting a python error and the process never finishes.I searched through the forum and it said that this was a known error and thatthere was a patch. When I installed the patch I got the exact same error.
The error message is: “ValueError: operands could not bebroadcast together with shapes (4,) (3,)” The link to the forum post is: https://secure-web.cisco.com/1BI_B41UWHwWJM3wQhzsqKLiN64Mdzk_AasgGunt7xAFi2Ti_IjaFqr8pVIuvUSD-ZLVEYI580vCnKVFO3EYgxKHmRJ2JwpJgt3IrlnVqXehDvlnA8m_QLcspvwOdEyuleG-SRP1hVpkuenwO4m4bfOK032XeTJ-p-yONPUHX8tZqDwR92JwPKU0O4ndK6mrXvnLvHl5tb0-tWBv59QOli-_OgfEo4ussU6uuv1voORx52Y1Cv4lPDV1kOknbYt_fapRm5e5mIgyQlFZfvQH2LXhv8ygBuozck_eNWt6s8tElJMnagVvzHCElOjzFYRnL_c_5eZh4VSDBJvRl1YwX7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg73652.html We tried running it on the test subject “bert” just to makesure the issue is not with our test scan and I got the same error. We are getting the erroreven after installing the patch. Here are the details of the commandline I used to run it and the error message: Command line: mri_sclimbic_seg --s bert --o/usr/local/freesurfer/7.3.2-1/subjects/bert/mri/mri_sclimbic_seg.mgz--write_volumes --write_qa_stat Error: Traceback (most recent call last): File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg",line 1049, in <module> main() File"/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line232, in main segmenter.process_files(**params) File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg",line 578, in process_files post, seg, vox_counts, volumes,mean_probs = self.segment(image) File"/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line498, in segment conformed = self.preprocess(image) File"/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line490, in preprocess processed =image.conform(shape=(*self.inshape, self.nchannels), voxsize=1.0,orientation='RAS', dtype='float32', copy=False) File "/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py",line 574, in conform conformed = conformed.reshape(shape,copy=False) File"/usr/local/freesurfer/7.3.2-1/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 withshapes (4,) (3,) We are beginning to study professional and amateur fighters, and we suspect that shearing/disruptions to the septum pellucidum may have downstream consequences to the connectivity/DTI measures in the septal nuclei, mammilary bodies, etc. Thanks in advance for any help or comments you can provide. Sincerely -Randy
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