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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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
https://secure-web.cisco.com/1uArc0AorFXAXMtq_4IuzUoFDzWIa9O6aV2zVC7494pyX9A144pqessRN-oRAvz7DHpuouU_Rz2M0dDbSngumE7vUNLQgV7ITrT-FrNL4bXmLLV4qnxTznIYD1GXWA-ZF7sM-9uQAUKAEFAfow9rQOR2yUqSvWbtKzmj4ffs1O4gIcgFIMrqkCJbdvdDNuo-V9putdrwCQnbU2cqH9hCWIaRSRZ_YrbvEKf59OAIGxOsI8UqCn0tYHUVu4LoEMwvWNW6ddvH9Hd-mNzBZo77x5nBdhjG47FS9_ww_M5LnVZ6Ethzhd2TDxSoz7YhaNgBj/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes<https://secure-web.cisco.com/1VyuG8OPfQJLnzsnjmw3QA-W2mRJoozUGm1eS1xFufA5MPMKU8WXqATE_8AWyUDbgmKUluXxRE2t6E383hRa6CL7af2DE-pusIvwW0m-QX-sZ2V6wZYivgHiWPmleggTFn0aQ_UpJX9qXK49NA9JfiLrTXStDgRB1WmTbQWrGM94316v8MK0BKCXWPUBvHzU_lRK0H7koGkrLqshk1h8j0umpdUYDdeh76A97AKttyNL_PrBe3Cs81UnhgXaSmkEJKluaskdDs3S6bjXvcphej0QPMAkqhWz5lGH5qk41yK9Nu1xBDfWFNUICsi3sGDfW/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes__;!!CvMGjuU!-U6zdB4EdaOM9AyFgmPs_Q9gf_VtOry1we2EavmLsNQilYq6gSHMhS-E1QRFydPIa_rX6AmSdb8PPVgq6N_L7T06FVVL$>
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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