External Email - Use Caution I really appreciate it. The installation is running!
Thank you, Lupita 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/1ZVC9BZ1-qmTPoQPQxkh3VCBrmAfuN09Mu3j5eR2oVlo16P8Jo4oaar0NRFTx4Dlc23d0XFrT7RSm2bGOft_r3ZTNmuXOV4W9GrpcgZ-yW04S-Zw_ro81pZInpufW5R1p7j8ikrYT4uCGYp9tFhPhqTMKFDWXvfMX1jCTYUSSbGP2LgwDEIzo32eF-VZNeN4iVAIUnwiG_kvIxoWvX6insxGcDKGKGjSuKa5BvTcJZCP6ysov8eAb9uJbq7CglAo1wk63emSBhMoTDjf7HJw8NNRUPJrIpk3epF-NHoN6TZ6pJSiymyuhdlM40D8w7xoKhRJNxkwhndDfnNGsxcQqXQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F8.0.0%2Ffreesurfer-macOS-darwin_arm64-8.0.0.pkg Then 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-beta The 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 2025 I 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> Date: Tuesday, February 11, 2025 at 12:36 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-beta There 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto:yanez-ramos.mariaguadal...@mayo.edu>> Date: Tuesday, February 11, 2025 at 11:53 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Recon-all error - release 8.0.0-beta Hello 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 arm64 recon-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 Max 3) 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 arm64 4) 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/1LMGxXCLw2HfspbmKSStURHrOGOw5rcboCZ8E7M16I3CHI-saCA4P1gqik0c27H2VlK69xF-ir5yjioh1zvOXpDyVK29ugvqT-F4NztYZNl1O1W1RODlfJUgw3e1E3_BmEMYXdUOa2vu_O1k6DdZllXt6l1Rvk0Sr3fUIy57ZSyeSw6-yqpSxtAGE2CH4SVjMTcJxnoW_DGT4s3ZRdwxPe7-2cuLaeQfQXu0NyD_3YlW6XeJL647AgvnKMZvnX8Dl2KjDMGBz82RtMsqX_aDs0-yEuyJPM-VaDY0sN4UtufBEsyGgAItwYdb9ZAQRjAkhVI71FwZXw69S8lZReBPeqg/https%3A%2F%2Fmail.nmr.mgh..harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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