Add brainageR v2.1

[JavierSanchez3]

Hello!

Is it possible to add brainageR v2.1?

https://github.com/james-cole/brainageR

Best regards!

[stebo85]

Dear @JavierSanchez3,

Yes, that's possible :) You could either write a new recipe for brainageR and propose it to our neurocontainers repo (e.g. based on https://github.com/fprados/brainageR_dockerfile ) or you build the brainageR_dockerfile, then upload the container to dockerhub and then use a simple recipe similar to fMRIprep (https://github.com/NeuroDesk/neurocontainers/blob/master/recipes/fmriprep/build.sh)

Can you give this is a go and let us know if you need any help?

Thank you
Steffen

[JavierSanchez3]

Hello Steffen,

I tried to create the build.sh script from the Dockerfile; however, an error appeared (see the attached document).

build_sh_attempt.txt

Do you recommend that I edit the original Dockerfile to try to correctly generate the build.sh script? In addition, I made another attempt by editing the Dockerfile, but further errors appeared when trying to install FSL 5.0.

Thanks for your support.

Best regards

[stebo85]

yes, these issues can be challenging and one option is to google the errors and troubleshoot them step by step,

e.g. libdeflate-dev

you can find out here https://pkgs.org/search/?q=libdeflate-dev which distros have this package - there you see that you could try ubuntu 20.04 as a base image instead of 16.04

[neurolabusc]

@stebo85 I have written a Python script for using brainager on neurodesk. It is pretty amazing - traditionally I have run brainager sequentially one individual at a time, but thanks to mcr on neurodesk I can run 96 instances at a time on my Threadripper, using a simple wrapper to read an entire BIDS folder. Neurodesk is really a game changer.

I think my script would be useful to others, but it will need integration from the neurodesk team. I tried to use the original brainager that has dependencies for spm12, Rscript, and fsl. The challenge is that "ml fsl" includes a huge number of tis own libraries and seems to wipe out Rscript. For this reason, my current script skips the creation of QA images (though this can be done in a separate pass).

If you email me, I can send you a link to my repository. It includes instructions and a sample T1 scan to demonstrate.

Once again, I am in awe of neurodesk. It really helps bring neuroimaging tools to scale.

[stebo85]

Great - will do this once i am back to work mid October