New subject: [EXTERNAL] Re: Recon-all error - release 8.0.0-beta

11 Feb 2025


      External Email - Use Caution
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/1gGVRcHPllNn9JWw3eUZMXCROYrPLvXC4ab7XhFI7Uwl7-w... 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 &lt;Yanez-Ramos..MariaGuadalupe@mayo.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Good to know, I am waiting for the new release.&nbsp;Thank you,&nbsp;Lupita&nbsp;From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu &lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of Huang, Yujing &lt;YHUANG43@mgh.harvard.edu&gt;
Date:&nbsp;Tuesday, February 11, 2025 at 13:38
To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Subject:&nbsp;[EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-betaThe new version will be announced &nbsp;in the next couple of days.&nbsp;From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu &lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp;On Behalf Of&nbsp;Yanez-Ramos, Lupita
Sent:&nbsp;Tuesday, February 11, 2025 2:31 PM
To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Subject:&nbsp;Re: [Freesurfer] Recon-all error - release 8.0.0-beta&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello&nbsp;Yujing,&nbsp;Thank you for your response.&nbsp;“There are no details of the error message in the log.”&nbsp;In the terminal the error message is:2 root error(s) found.&nbsp; (0) INVALID_ARGUMENT:&nbsp; input must be 4-dimensional[1,72,72,72,24]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[unet/unet_bn_down_0/FusedBatchNormV3/_16]]&nbsp; (1) INVALID_ARGUMENT:&nbsp; input must be 4-dimensional[1,72,72,72,24]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[{{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&nbsp; 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64&nbsp;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.&nbsp;Does your error look something like this?&nbsp; (0) INVALID_ARGUMENT:&nbsp; input must be 4-dimensional[1,72,72,72,24]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[unet/unet_merge_4/concat/_64]]&nbsp; (1) INVALID_ARGUMENT:&nbsp; input must be 4-dimensional[1,72,72,72,24]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]&nbsp;Yes it is.&nbsp;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?&lt;image001.png&gt;&nbsp;Thank you,&nbsp;Lupita&nbsp;From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of Huang, Yujing &lt;YHUANG43@mgh.harvard.edu&gt;
Date:&nbsp;Tuesday, February 11, 2025 at 12:36
To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Subject:&nbsp;[EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-betaThere are no details of the error message in the log.&nbsp;Does your error look something like this?&nbsp; (0) INVALID_ARGUMENT:&nbsp; input must be 4-dimensional[1,72,72,72,24]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[unet/unet_merge_4/concat/_64]]&nbsp; (1) INVALID_ARGUMENT:&nbsp; input must be 4-dimensional[1,72,72,72,24]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]&nbsp;If so, we fixed the error in the coming FS 8.0 release.&nbsp;Yujing&nbsp;&nbsp;From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp;On Behalf Of&nbsp;Yanez-Ramos, Lupita
Sent:&nbsp;Tuesday, February 11, 2025 1:23 PM
To:&nbsp;freesurfer@nmr.mgh.harvard.edu
Subject:&nbsp;[Freesurfer] Recon-all error - release 8.0.0-beta&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;From:&nbsp;Yanez-Ramos, Lupita &lt;Yanez-Ramos.MariaGuadalupe@mayo.edu&gt;
Date:&nbsp;Tuesday, February 11, 2025 at 11:53
To:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;
Subject:&nbsp;Recon-all error - release 8.0.0-betaHello FreeSurfer Developers,&nbsp;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.&nbsp;ERROR:Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan&nbsp; 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&nbsp;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.&nbsp;1) FreeSurfer version: FreeSurfer version 8.0.0-beta&nbsp;MacOS X darwin_arm64 (64b) PKG installer&nbsp;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&nbsp; 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm644) recon-all.log: see attached&nbsp;Thank you so much, I really need to use recon-all to complete my project.&nbsp;Have a great day,&nbsp;Lupita_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer