External Email - Use Caution OK, thanks for the quick feedback. I did not see an attached log. Maybe you could cut and paste the end or section with the error and forward it along so we can see the last few commands in the pipeline that ran. - R.
On Feb 11, 2025, at 20:16, Yanez-Ramos, Lupita <yanez-ramos.mariaguadal...@mayo.edu> wrote: External Email - Use Caution The recon-all was running for around an hour. But it fails again, but in different way (I think).Now the process advanced more. The error in the terminal is: Loading surf /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.white.preaparcFound 0 label voxelsERROR: found no voxels matching id 1 ERROR:Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 recon-all -s sub-MSEL02220 exited with ERRORS at Tue Feb 11 19:09:36 CST 2025 The error log is attached. From: fsbuild <fsbu...@contbay.com> Date: Tuesday, February 11, 2025 at 17:44 To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-beta Hello Lupita, Although the 8.0.0 release has not yet been officially announced, you could try downloading it from the link listed below. I would first remove your existing beta install with, $ cd /Applications/freesurfer/8.0.0-beta$ sudo bash uninstall.sh… answer Y to uninstall ... Then download the package installer via this link and run it.https://secure-web.cisco.com/1bTPb6RNd1UFnPCoRK-ER5lb8yUI8XAd2gN-0eQQx3-dZlpCQ9-_Cqun8H3gYfW4nQPAngFNDWDiDdzO9Nf8SUPD04JcsIH2sUunytm_7USloftotoBq1pn_pIgDCazn48GDyju7XnWEehMz8I7JYYCZZnF01X3ws50IxaeANIZIwn16GrR8IIagWT9quxkIRzha09mwaQ8htDULTHrJIDSCnK0rB5TMvHxtgyMrgByskCimiAa1uuxksn2s7zXVH0aaZTYMTlkZUH12L6d2ptkCS_J-ViFZscz5icndgAICdVLdP7_M6OSBXRKBxUT-XfVQz-fTGdrtfwr_x-bejxA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F8.0.0%2Ffreesurfer-macOS-darwin_arm64-8.0.0.pkgThen you should end up with /Applications/freesurfer/8.0.0 and use that for FREESURFER_HOME Please let us know if you run into any issues. - R On Feb 11, 2025, at 14:42, Yanez-Ramos, Lupita <yanez-ramos.mariaguadal...@mayo.edu> wrote: External Email - Use Caution Good to know, I am waiting for the new release. Thank you, Lupita From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu> Date: Tuesday, February 11, 2025 at 13:38 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-betaThe new version will be announced in the next couple of days. From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Yanez-Ramos, Lupita Sent: Tuesday, February 11, 2025 2:31 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all error - release 8.0.0-beta External Email - Use Caution Hello Yujing, Thank you for your response. “There are no details of the error message in the log.” In the terminal the error message is:2 root error(s) found. (0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] [[unet/unet_bn_down_0/FusedBatchNormV3/_16]] (1) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]0 successful operations.0 derived errors ignored. [Op:__inference_predict_function_1146]ERROR:Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 recon-all -s sub-01 exited with ERRORS at Tue Feb 11 13:12:04 CST 2025I can’t see any other information, Only the log that I attached in the las email and the info in the terminal.I attached the terminal text. Does your error look something like this? (0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] [[unet/unet_merge_4/concat/_64]] (1) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] Yes it is. If so, we fixed the error in the coming FS 8.0 release.Just I used this version, is there other release? How can I have the fixed release?<image001.png> Thank you, Lupita From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <yhuan...@mgh.harvard..edu> Date: Tuesday, February 11, 2025 at 12:36 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-betaThere are no details of the error message in the log. Does your error look something like this? (0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] [[unet/unet_merge_4/concat/_64]] (1) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] If so, we fixed the error in the coming FS 8.0 release. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Yanez-Ramos, Lupita Sent: Tuesday, February 11, 2025 1:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all error - release 8.0.0-beta External Email - Use Caution From: Yanez-Ramos, Lupita <yanez-ramos.mariaguadal...@mayo.edu> Date: Tuesday, February 11, 2025 at 11:53 To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Recon-all error - release 8.0.0-betaHello FreeSurfer Developers, I'm attempting to run recon-all and recon-all-clinical, but it is the first time that I used this since I changed my MacBook. ERROR:Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81..4~3/RELEASE_ARM64_T6041 arm64recon-all -s sub-01 exited with ERRORS at Tue Feb 11 10:33:15 CST 2025 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: FreeSurfer version 8.0.0-beta MacOS X darwin_arm64 (64b) PKG installer 2) Platform: macOs Sequoia 15.3. Chip Apple M4 Max3) uname -a: Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm644) recon-all.log: see attached Thank you so much, I really need to use recon-all to complete my project. Have a great day, Lupita_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1hSLlW0Tx4WU9rOAvjc2c5Hc9vZ2n6LY6Sxfx-6SykHA-_uuYtAj9nKIiDLRmYURYOQU7fGeUu9IihvUkQDUnpzYi6EVN4GY9GrI1QG_jQzuw1I9cgzC3Gr_CMCumdjnUBFB7R-sNIGWlzAFAAJM4MUSZuXcGG0MDkFLuVEM6jO2aZ51xR-Ad6BUksaNm-yooQdQuhkk_sqxAI16O7KOW4DPdElphkK7aEEW8qJazLwotUV5ZRJ7DKoi9UAnyrA7ZqcbtL5BY8kFSWL9X99Jd1ppfpwa0BYx_M3QGu7ysi3NbzAHElQIOhxF4uF1g7SzHzmZpknybQXfQugw1alFb3w/https%3A%2F%2Fmail.nmr.mgh..harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer%26nbsp;<recon-all.log>_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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