External Email - Use Caution

After replacing mri_sclimbic_seg with the patch notes, I get further downstream, but still encounter an error:

/usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg --s GP0017-bpd/ --conform

Excluding seg [853]

Using CPU

Using 1 thread(s)

Loaded lookup table /usr/local/freesurfer/dev7/models/sclimbic.ctab

Loaded population stats /usr/local/freesurfer/dev7/models/sclimbic.volstats.csv

nb_labels 14

Loaded model weights /usr/local/freesurfer/dev7/models/sclimbic.fsm+ad.t1.nstd00-50.nstd32-50.h5

Using subject directory /mnt/V/Datasets/BSNIP2/Processing/Finished_q3

Computed eTIV from talairach

Segmenting subject GP0017-bpd/ 1/1

Loaded input image from /mnt/V/Datasets/BSNIP2/Processing/Finished_q3/GP0017-bpd/mri/nu.mgz

XXX lineno: 497, opcode: 255

Traceback (most recent call last):

File "/usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg", line 1049, in <module>

main()

File "/usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg", line 232, in main

segmenter.process_files(**params)

File "/usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg", line 578, in process_files

post, seg, vox_counts, volumes, mean_probs = self.segment(image)

File "/usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg", line 497, in segment

self.reset_timer()

SystemError: unknown opcode

Exception ignored in tp_clear of: <class 'type'>

TypeError: object.__init__() takes exactly one argument (the instance to initialize)

Exception ignored in tp_clear of: <class 'dict'>

TypeError: object.__init__() takes exactly one argument (the instance to initialize)

Segmentation fault

Victor Zeng

Beth Israel Deaconess Medical Center

Keshavan Lab

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Sunday, October 16, 2022 5:24 PM

To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>

Subject: [External] Re: [Freesurfer] Question about sclimbic

This is a known bug. Please see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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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