On 20 Dec 2022, at 04:29, 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:

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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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