Error calling FSL-BET

[Francesco Molla]

Dear cpac developers and users,

I am experiencing a strange error when running the latest releases of C-PAC (v 1.8.2,3,4).
The pipeline crashes while performing the brain extraction on the functional files, saying that it cannot find the binaries for fsl-bet & co, although the $FSLDIR variable is correctly specified in the YAML file.

I overcame this issues by running the command that failed outside of the container and re-running the whole pipeline. However this is very time consuming and not optimal, so I was wondering if anyone could help me figure out what is going on.

I am attaching the crash file, the pipeline configuration and data configuration file.

Best,
Francesko

[Francesko Molla]

Also, it would be nice to have a way to control the options for the flirt call for the initial ACPC alignment since it often fails with the default settings.

Best,

Francesko

On 29 Aug 2022, at 16:15, Francesco Molla <molla.f...@gmail.com> wrote:



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[Francesco Molla]

Thank you for fixing the previously reported bug! :)

[amyguti...@gmail.com]

Hello, 

So that I can help you better, can you send me your full run command you used (i.e. docker run ...)? 

And as for the options with ACPC alignment, are you talking about: 

acpc_alignment: 

   FOV_crop: robustfov 

This FOV_crop can be changed to flirt. Check out our default_pipeline.yml file for reference. 

[Francesco Molla]

Hello,

here is the command that I run:

singularity run /${home}/cpac_images/c-pac\:release-v1.8.2.sif /${home}/site-newcastle/ /${home}/results participant --pipeline_file /${home}/pipeline_file.yml
I know it is not the latest release, but I need to keep the processing consistent with my previous work, and the porblem arises even with the 1.8.4 release as I have verified.

> This FOV_crop can be changed to flirt. Check out our default_pipeline.yml file for reference.

As far as I understand this is for cropping in the z-direction, using either fslroi or robustfov.
What I mean is if there is a way to choose the cost functions, search radius, etc etc for the ACPC alignment.
Or should I just typein the flirt command without inputs in the FOV_crop field?

Best,
Francesko

[Amy Gutierrez]

Hello, 

What version of singularity are you using? That error has been seen in versions previous to version 2.1. If your singularity version is older than 2.1, try updating the version and then creating the image again. To use CPAC version 1.8.2, you can create the singularity image with 

singularity pull docker://fcpindi/c-pac:release-v1.8.2-DEPRECATED

As for the ACPC alignment, for monkey data, it is recommended to use flirt and not robustfov. Here are the lines of our code that pertain to acpc alignment being used with flirt. It would be the same as running command flirt -in "${Input}" -applyxfm -ref "${Input}" -omat "$WD"/roi2full.mat -out "$WD"/robustroi.nii.gz

Additionally, we have a monkey pipeline config (--preconfig monkey) if you'd like to take a look at our pipeline options and cross compare with your pipeline.

Please let me know if you have any additional questions!!

[Amy Gutierrez]

Additionally, you can also change your FSLDIR in your pipeline_file.yml (line 140) to FSLDIR (example). This will use CPAC's FSL.