On Feb 11, 2025, at 20:16, Yanez-Ramos, Lupita <Yanez-Ramos.MariaGuadalupe@mayo.edu> wrote:

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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.preaparc

Found 0 label voxels

ERROR: 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 <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://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/8.0.0/freesurfer-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.MariaGuadalupe@mayo.edu> wrote:

 

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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

 

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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.edu <freesurfer-bounces@nmr.mgh..harvard.edu> on behalf of Huang, Yujing <YHUANG43@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-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.edu <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.edu
Subject: [Freesurfer] Recon-all error - release 8.0.0-beta

 

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From: Yanez-Ramos, Lupita <Yanez-Ramos.MariaGuadalupe@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-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

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