Running micapipe_cleanup and other scripts

MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below

http://micapipe.readthedocs.io

GNU General Public License v3.0

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Running micapipe_cleanup and other scripts #38

Closed mrribbits closed 2 years ago

mrribbits commented 2 years ago

What are you trying to do?
Trying to run micapipe_cleanup (and other scripts such as micapipe_qc) from docker on my local machine (or singularity on my HPC). It's probably very simple but I just don't know how. I am able to run the main mica-pipe and its processing modules with no problem, but how do I call these additional scripts in a docker (and singularity) command? It would be great to add an example in the Installation/Usage sections for newbs like me. Thank you!

mrribbits commented 2 years ago

I got it now, thanks. I knew it was something simple just had trouble finding it. Here's an example for other newbies that may be wondering the same: singularity exec ./micapipe_v0.1.2.simg /opt/micapipe/functions/micapipe_cleanup -h