CONN toolbox Update

[AndreaCoca-Pulido]

Hi, I'm checking that there is a new version of CONN toolbox (22.a) Is it possible to include this in neurodesk? Thanks a lot! best, Andrea

[stebo85]

Dear @AndreaCoca-Pulido,

The 22.a version of the conn toolbox was unfortunately not released yet as a standalone version by the conn toolbox developers. The latest version available as a standalone is 21a:

https://www.nitrc.org/frs/?group_id=279

To integrate nicely on Neurodesk we require the standalone version that doesn't require a matlab license: These are indicated with _glnxa64, such conn21a_glnxa64.

There are a few paths forward:

• we can add version 21a if this is helpful to you
• you can contact the conn toolbox developers and ask if they could release a standalone version of 22a
• you could download the 22a version yourself and run it using Matlab and using your own Matlab license

What would work best for you?

Kind regards Steffen

[stebo85]

Dear @AndreaCoca-Pulido,

I created a forum post here to ask for a release of the standalone version: https://www.nitrc.org/forum/forum.php?thread_id=14696&forum_id=1144

Kind regards Steffen

[stebo85]

I tried building 21a, but the standalone version doesn't work:

conn-21a:~$ conn Initializing MATLAB Runtime version 9.10 Loading MCR. Please wait... Warning: Removing "/home/jovyan/.mcrCache9.10/conn_d0/project/busplab/software/spm12/external/fieldtrip/compat/matlablt2016b" from your path. See http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path/ Error using fullfile (line 103) All inputs must be strings, character vectors, or cell arrays of character vectors.

Error in runtimeInitializationChecks (line 12)

MATLAB:fullfile:InvalidInputType

[AndreaCoca-Pulido]

Hi Steffen,

Thank you so much for your interest and concern in helping me with this. It looks like I would have to wait until they release the standalone or answer the forum. Hopefully It will be soon.

Thank you very much again,

Kind regards,

Andrea

Andrea

Andrea Coca Pulido University of Granada Biomedicine PhD Student Department of Physical Education and Sports Granada, Spain. Research Group: http://profith.ugr.es/ Twitter: @acocapulido https://twitter.com/acocapulido?lang=es

El lun, 23 oct 2023 a las 2:12, Steffen Bollmann @.***>) escribió:

I tried building 21a, but the standalone version doesn't work:

conn-21a:~$ conn Initializing MATLAB Runtime version 9.10 Loading MCR. Please wait... Warning: Removing "/home/jovyan/.mcrCache9.10/conn_d0/project/busplab/software/spm12/external/fieldtrip/compat/matlablt2016b" from your path. See http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path/ Error using fullfile (line 103) All inputs must be strings, character vectors, or cell arrays of character vectors.

Error in runtimeInitializationChecks (line 12)

MATLAB:fullfile:InvalidInputType

— Reply to this email directly, view it on GitHub https://github.com/NeuroDesk/neurocontainers/issues/500#issuecomment-1774242224, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWIC5BBCHXVUTNUBG4WK4NLYAWY67AVCNFSM6AAAAAA6HEPFQOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZUGI2DEMRSGQ . You are receiving this because you were mentioned.Message ID: @.***>

[stebo85]

Dear @AndreaCoca-Pulido,

There has unfortunately not been a reply on the forum - can you contact the authors of the conn toolbox as well and ask for a compiled version?

Alternatively, you can run conn toolbox in Matlab using your institutional license.

Kind regards Steffen

[AndreaCoca-Pulido]

Thank you very much, I will do that. Andrea

Andrea Coca Pulido University of Granada Biomedicine PhD Student Department of Physical Education and Sports Granada, Spain. Research Group: http://profith.ugr.es/ Twitter: @acocapulido https://twitter.com/acocapulido?lang=es

El dom, 12 nov 2023 a las 23:08, Steffen Bollmann @.***>) escribió:

Dear @AndreaCoca-Pulido https://github.com/AndreaCoca-Pulido,

There has unfortunately not been a reply on the forum - can you contact the authors of the conn toolbox as well and ask for a compiled version?

Alternatively, you can run conn toolbox in Matlab using your institutional license.

Kind regards Steffen

— Reply to this email directly, view it on GitHub https://github.com/NeuroDesk/neurocontainers/issues/500#issuecomment-1807257336, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWIC5BFFMXVAZEMDN5KA46LYEFCEHAVCNFSM6AAAAAA6HEPFQOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBXGI2TOMZTGY . You are receiving this because you were mentioned.Message ID: @.***>

[AndreaCoca-Pulido]

Dear Steffen Bollmann,

This is the response I got from the authors of the conn toolbox:

"Hi Andrea

I have now uploaded to NITRC CONN's version 2022a compiled for linux machines. The installation files/instructions are available at

https://web.conn-toolbox.org/resources/installation/standalone-linux https://web.conn-toolbox.org/resources/installation/standalone-linux

Tthe CONN 2022a installation files are now available at:

https://www.nitrc.org/frs/download.php/13733/conn22a_glnxa64.zip https://www.nitrc.org/frs/download.php/13733/conn22a_glnxa64.zip

and the corresponding version of MCR is now MCR 2022a (9.12), which can also be downloaded from:

https://www.nitrc.org/frs/downloadlink.php/13734 https://www.nitrc.org/frs/downloadlink.php/13734

Let me know if you need any additional information and/or if you run into any issues

Best Alfonso"

Does this solve the problem you had with the installation?

Thank you very much for everything,

Andrea

Andrea Coca Pulido University of Granada Biomedicine PhD Student Department of Physical Education and Sports Granada, Spain. Research Group: http://profith.ugr.es/ Twitter: @acocapulido https://twitter.com/acocapulido?lang=es

El dom, 12 nov 2023 a las 23:08, Steffen Bollmann @.***>) escribió:

Dear @AndreaCoca-Pulido https://github.com/AndreaCoca-Pulido,

There has unfortunately not been a reply on the forum - can you contact the authors of the conn toolbox as well and ask for a compiled version?

Alternatively, you can run conn toolbox in Matlab using your institutional license.

Kind regards Steffen

— Reply to this email directly, view it on GitHub https://github.com/NeuroDesk/neurocontainers/issues/500#issuecomment-1807257336, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWIC5BFFMXVAZEMDN5KA46LYEFCEHAVCNFSM6AAAAAA6HEPFQOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBXGI2TOMZTGY . You are receiving this because you were mentioned.Message ID: @.***>

[stebo85]

Dear @AndreaCoca-Pulido ,

Great :) I now added this new version to Neurodesk. You need to click the "Update" button in the menu to make the new version visible in the menu system:

Let me know if everything works as expected!

Thank you Steffen

[AndreaCoca-Pulido]

Dear @stebo85,

It seems that something is not working well in the new installation of the conn22a. I have detected several issues:

1. When I update neurodesk in this Mac (characteristics in the photo), neither the conn22a nor the connGUI22a do not appear so that i can not run it.

2. When I update neurodesk in this Macbook (characteristics in the photo), the conn22a and the connGUI22a appear but when i click on them, it seems that just the conn22a works but not the GUI (the one that i need) and i try to open it through bash using ml conn/22a and it replies me with this error:

conn-22a:~$ ml conn/22a bash: /usr/share/lmod/lmod/libexec/ml_cmd: No such file or directory

So i dont really know what it is happening. If you could help me to solve this problem it would be very helpful.

Thank you so much, Andrea

[stebo85]

Dear @AndreaCoca-Pulido ,

We just released a new version of Neurodesk (Neurodeskapp 1.3.0, Docker image version vnmd/neurodesktop:2023-11-28) which should fix your problem on both Mac systems you have. Can you test and confirm?

Thank you Steffen

[AndreaCoca-Pulido]

Dear @stebo85,

It does not appear in the Mac Pro, however It appears already in my Macbook Pro but it works a little slow...

I dont really know what it is happening with the Mac...

Thank you so much!

Andrea

[stebo85]

Dear @AndreaCoca-Pulido ,

1) can you check which version of neurodesk you are running? 2) can you check if you enabled Rosetta in your docker settings?

thank you Steffen

[AndreaCoca-Pulido]

Dear @stebo85

1. I am trying to find where to see this info.
2. I think i did not enable it because i found this message:

But I dont know why it is working so slow knoe,

I´ll answer to 1. whenever the PC´ll let me,

Thank you so much,

Andrea

[stebo85]

1. you can see the neurodesk app version by clicking on about - it needs to be 1.3.0 2) you need Rosetta enabled in docker - otherwise it’s 80% slower. So update and then enable it.

Thank you

Steffen

--

W: https://mri.sbollmann.nethttps://mri.sbollmann.net/ | W: https://www.neurodesk.orghttps://www.neurodesk.org/ | T: https://twitter.com/sbollmann_MRI | G: https://github.com/stebo85

Book meeting: https://calendly.com/s-bollmann/meeting

---

From: AndreaCoca-Pulido @.> Sent: Friday, December 8, 2023 8:45:16 PM To: NeuroDesk/neurocontainers @.> Cc: Steffen Bollmann @.>; Mention @.> Subject: Re: [NeuroDesk/neurocontainers] CONN toolbox Update (Issue #500)

Dear @stebo85https://github.com/stebo85

1. I am trying to find where to see this info.
2. I think i did not enable it because i found this message: Captura.de.pantalla.2023-12-08.a.las.11.43.41.png (view on web)https://github.com/NeuroDesk/neurocontainers/assets/93335172/8e4101a2-bd99-422b-813c-432e656c8c72

But I dont know why it is working so slow knoe,

I´ll answer to 1. whenever the PC´ll let me,

Thank you so much,

Andrea

— Reply to this email directly, view it on GitHubhttps://github.com/NeuroDesk/neurocontainers/issues/500#issuecomment-1846945887, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA6V2W2PBLRBNGCZR6UDBNLYILVTZAVCNFSM6AAAAAA6HEPFQOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBWHE2DKOBYG4. You are receiving this because you were mentioned.Message ID: @.***>

[AndreaCoca-Pulido]

My neurodesk app version is 1.3.0 so it is fine. I think rosetta is know enabled:

[stebo85]

Great :) is everything working as expected now?

[AndreaCoca-Pulido]

I could not check it in the Mac PRO because we are having some internal issues. However, Although i did what you told me to do to make it work faster, it still goes so slow, dont know why :((

[stebo85]

Can you copy the data to your homedirectory inside neurodesk and try again? Can you also describe what exactly you are doing and what exactly is slow?

[stebo85]

Dear @AndreaCoca-Pulido,

Can you confirm that everything is working for you now, so I can close this issue?

Thank you Steffen

[AndreaCoca-Pulido]

oh sorry, I totally forgot that everything was working great! Thank you so much! You have been so helpful😀

[stebo85]

Wonderful- thank you for confirming:) what solved the speed issues you were seeing?

[AndreaCoca-Pulido]

I guess freeing up memory space helped a bit hahahaah We are running many analyses and generating many heavy documents....

[stebo85]

Ok, that makes sense! Thank you for reporting back and glad to hear it’s working now as expected:)