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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 --
This is a known bug. Please see 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 --
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
This is a known bug. Please see https://secure-web.cisco.com/1uArc0AorFXAXMtq_4IuzUoFDzWIa9O6aV2zVC7494pyX9A...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 --
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1x6nTuNHvMbKlOaLXM6O1lsbalua_tFw3SzMFq-vWsaX6RK...https://secure-web.cisco.com/13XWCGI-oS4FgTctijM3zPRMPtaJWEUOEeMyHCeDn5sZVXMCmkgDqxe37exX_QKiISOsZJynsJZv3l6lc9FHXxDT-iNUojpEpC6i4sJ8MO_98opk7JGZQBFqszIFvaritn37Z9ZqpH4-0OnSNM46PFIIsH3l2LeRxq5F_FxNTdyiQdkwVhMTozaTsUmPk8fSnHlysngFv3iO-0nkxd0VP1Qzy0AZXlqKsMdBvfGAZifnxPDNYrYJjRooBZ_XjoUyszSJV21ALwpVdKAAYFEc_BXDewOlLiexp6qm3dI0AOtBUqHcFSfZC1lLOwv05-zKj/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!CvMGjuU!-U6zdB4EdaOM9AyFgmPs_Q9gf_VtOry1we2EavmLsNQilYq6gSHMhS-E1QRFydPIa_rX6AmSdb8PPVgq6N_L7Zkn3_Or$
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
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/ReleaseNoteshttps://secure-web.cisco.com/1GVUvssivpgTLC3JqpnUuYfyz7_C0l_OZzy-eHEDYuhGleI_PpTeZ89VSsD-V25UkNwDiBpnsgGwcE_QFdLCBcoKStuwPOW9Uicn4EX6ApHtgLpUC5BonCGymx4T5cyeanfQ0CoZOBfmEsv_5MTbChb5HtMToDbOrSlubce9Qenc-hrcx8tRxbZ_H6PooXNYX_1Zh-0Q9XCWrWD790AM-W3d4Mv1yIjdf53R-zmDR2_DeXZ2bVHMZjAXD-zQTlPc3wcyBTDFlqEB4A6mauTwRvfr4Dydk9T2WQApGp-WYmZsukBU4k1HI2JJJ_VMP04kc/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes__%3B%21%21CvMGjuU%21-U6zdB4EdaOM9AyFgmPs_Q9gf_VtOry1we2EavmLsNQilYq6gSHMhS-E1QRFydPIa_rX6AmSdb8PPVgq6N_L7T06FVVL%24 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 --
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1Pet-YQqAn7x_LaB-ekHkJy1v5wTqDCp0IFRB4AggOcYJuToqo_61X6h2z-Cc5II6FzVKpqR-3uELUGDg8mDUXLQ6syigK-Zerch6vbM6IUjO2V8mSvI01C07wIZh1XYIrSPnJZH3Lf24_qeZZjDG15cx6dr80mWvKkcaB4-6xLEBIGzNVp9F8iKDejvE1ehqF8XlSxQVEwkvFj3xsW5XdrM3UM66Vbc7F9u3esH2Q1Yjbk6AKN0-dkoo89mCVHP664W6gpRK_7WwnRBy8_Sx-73KCkpjaNPWRD8aF26LvCBh7KbkTRCBWkDY84G_zEbP/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21CvMGjuU%21-U6zdB4EdaOM9AyFgmPs_Q9gf_VtOry1we2EavmLsNQilYq6gSHMhS-E1QRFydPIa_rX6AmSdb8PPVgq6N_L7Zkn3_Or%24
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Kumar, Avnish -
Zeng, Victor (BIDMC - Keshavan - Psychiatry)