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faskowit / app-multiAtlasTT

brainlife.io version of maTT
MIT License
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module: command not found #16

Closed soichih closed 3 years ago

soichih commented 3 years ago

This is for the old version (Multi-Atlas Transfer Tool - old) but I've seen users running into this error message

+ module load freesurfer
./main: line 36: module: command not found

Not all resources have module command, and we also don't know which version of freesurfer gets loaded, so maybe we should not rely on module?

faskowit commented 3 years ago

I thought I was able to catch the error with the || on this line: https://github.com/faskowit/app-multiAtlasTT/blob/master/main#L36

soichih commented 3 years ago

That is true.. I must have picked the wrong error message when I was looking.. I will reopen this when I find the failing job again.

faskowit commented 3 years ago

But there is another good point here... for future work, it probably won't be ideal to support two versions of the maTT app. After I finish my dissertation writing... I should revisit making the surfaces work with the new freesurfer-mini container...

Maybe the answer could be... run reprozip on it one time with the full FreeSurfer docker... make a docker out of that reprozip'ed container... then make a new dockerfile that imports all the atlas data (therefore "adding that data back in").

soichih commented 3 years ago

That sounds good @faskowit

About reprozip.. @bacaron and I were discussing a need to create a container that has fsl/ants/mcr all together. The size of the container will be extreme, and I was wondering if we could reprozip. If you try reprozip, I'd like to learn from you how we can use it to reduce the container size.