Hi Randy and Yann,
For this fix you will have to update the surfa package that ships with Freesurfer. You can do this by: fspython -m pip install --upgrade surfa
Best, Avnish ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yann Quidé yannquide@gmail.com Sent: Tuesday, December 20, 2022 3:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: daedalus39@aol.com daedalus39@aol.com Subject: Re: [Freesurfer] mri_sclimbic_seg patch issue?
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Hi all,
I have the same issue on Ubuntu 22.04, patch is installed. Many thanks,
Yann
On 20 Dec 2022, at 04:29, daedalus39@aol.commailto:daedalus39@aol.com wrote:
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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 run mri_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 that there was a patch. When I installed the patch I got the exact same error.
The error message is: “ValueError: operands could not be broadcast together with shapes (4,) (3,)” The link to the forum post is: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73652.htmlhttps://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 make sure the issue is not with our test scan and I got the same error.
We are getting the error even after installing the patch. Here are the details of the command line 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", line 232, 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", line 498, in segment conformed = self.preprocess(image) File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 490, 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 with shapes (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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