External Email - Use Caution
I really appreciate it. The installation is running!
Thank you,
Lupita
From: fsbuild fsbuild@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-qmTPoQPQxkh3VCBrmAfuN09Mu3j5eR2oVlo16P... 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.MariaGuadalupe@mayo.edu wrote:
External Email - Use Caution
Good to know, I am waiting for the new release.
Thank you,
Lupita
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Tuesday, February 11, 2025 at 12:36 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yanez-Ramos, Lupita Sent: Tuesday, February 11, 2025 1:23 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.MariaGuadalupe@mayo.edumailto:Yanez-Ramos.MariaGuadalupe@mayo.edu> Date: Tuesday, February 11, 2025 at 11:53 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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-...