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HBClab / RestingState

Scripts to preprocess resting state data and extract ROI-ROI correlations and voxel-wise ROI seedmaps
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Why do we need freesurfer? #101

Closed jdkent closed 5 years ago

jdkent commented 5 years ago

Summary

The containers are big and freesurfer is the largest contributor to that. What freesurfer commands do we run and how much from freesurfer do we need?

Actual behavior

Containers take a long time to build and move

Expected behavior

Containers should be "light-ish" weight when possible

How to replicate the behavior

either build a container locally or pull from dockerhub.

Script/Workflow details

Please put URL to code or code here (if not too long).

tbweng commented 5 years ago

@jdkent Good point. I think freesurfer was a prerequisite because at some point your MBA skull stripping algorithm (which needs fs) was wrapped into these scripts. But based on that logic, MBWSS would have been a prereq as well...hmm :anguished:

A quick skim through the scripts suggests freesufer isn't needed. Will try a test run without freesufer loaded to verify.