Request to Add Latest Version of CAT12

[JavierSanchez3]

Hello,

I hope you are doing well. I was wondering whether you could add the latest version of CAT12 (CAT12.9 (r2577))?

https://github.com/ChristianGaser/cat12/releases/tag/12.9

I appreciate your assistance.

Best regards and thanks for all your support.

[stebo85]

That is possible. Can you propose this change through a pull request to the build recipe in the neurocontainers repository?

[JavierSanchez3]

Hello @stebo85 ,

I ran Guacamole and then loaded the following modules in the Terminal:

ml spm12/r7771
ml cat12/12.9

However, when I run "spm12", cat12 did not appear in the toolbox options.

I also tested loading matlab/2024b previously (I don't know if that is correct), but a error message appeared when running "spm12":
FATAL: container creation failed: mount hook function failure: mount /home/jovyan->/opt/matlab/R2024b/licenses error: while mounting /home/jovyan: destination /opt/matlab/R2024b/licenses doesn't exist in container

[stebo85]

do not load spm12 or matlab beforehand! Both are integrated in the cat12 container.

From a normal terminal within the guacamole neurodesktop you can either run :

(base) jovyan@neurodesktop-:~$ ml cat12/12.9
(base) jovyan@neurodesktop-:~$ run_spm12.sh /opt/mcr/v93/

or you go to the application menu -> Neurodesk -> Image Segmentation -> Cat12

Let us know if this works :)

[JavierSanchez3]

Hello @stebo85

First, I tried to follow your instructions to open cat12GUI 12.9, but, cat12GUI12.9 and cat12 12.9 did not appear.

Then, I executed the following code:

(base) jovyan@neurodesktop-:~$ ml cat12/12.9 (base) jovyan@neurodesktop-:~$ run_spm12.sh /opt/mcr/v93/

However, the following error appeared when loading SPM12 in the Terminal

SPM12: v7771 16:10:02 - 07/03/2025

Initialising SPM : ..Failed to open file '/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_check_SPM.m'. Details: 'File stream is closed. The following flags are set: failbit.'
Previously accessible file "/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_check_SPM.m" is now inaccessible.

Error in cat_conf_tools>conf_stat_check_SPM (line 3254)

Error in cat_conf_tools (line 172)

Error in tbx_cfg_cat (line 108)

Error in spm_cfg_static_tools (line 3)

Error in spm_cfg (line 84)

Error in cfg_mlbatch_appcfg_1 (line 9)

Error in cfg_mlbatch_appcfg_master

Error in cfg_util>local_initapps (line 1453)

Error in cfg_util (line 743)

Error in spm_jobman (line 189)

Error in spm (line 335)

Error using waitforallfiguresclosed (line 9)
Error while evaluating DestroyedObject Callback.

Then, I tried updating neurodesk to the latest version (1.10), however, none of the existing modules loaded.

[stebo85]

Dear @JavierSanchez3 -

The gui entry didn't appear for you because you didn't click on update in the menu beforehand.

The next error you see is a bug in cat12. I opened an issue in the cat12 repository and once the maintainers of cat12 fix it we can update again.

[stebo85]

ChristianGaser/cat12#38

[stebo85]

It’s not yet build correctly. Thank you Steffen

…

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________________________________ From: JavierSanchez3 ***@***.***> Sent: Thursday, March 6, 2025 7:27:23 PM To: NeuroDesk/neurodesk.github.io ***@***.***> Cc: Steffen Bollmann ***@***.***>; Comment ***@***.***> Subject: Re: [NeuroDesk/neurodesk.github.io] Request to Add Latest Version of CAT12 (Discussion #482) Hello, Thank you for the help. I cheked the loaded section, but cat12/r2577 did not appear. Is there anything I can do? (base) ***@***.***:~$ ml cat12/r2577 Lmod has detected the following error: The following module(s) are unknown: "cat12/r2577" Regards :) — Reply to this email directly, view it on GitHub<#482 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AA6V2WYMCBAT2U6HDZB32HD2TAIHXAVCNFSM6AAAAABYKAPUYOVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTENBRGE3TQMA>. You are receiving this because you commented.Message ID: ***@***.***>