Hi Victor,
I have not been able to recreate this error. Would you be able to share some sample image that I can use to recreate this error?
Best, Avnish ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu Sent: Wednesday, October 19, 2022 10:40 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Question about sclimbic
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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
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On 10/14/2022 1:46 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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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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