dmriprep
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nipy
MOVED TO https://github.com/nipreps/dmriprep
Right now, we have to drop into our docker image. In the long run, we'd also like to run this from the command line, without dropping in (see #72).
Get a small data set and run the whole thing end-to-end on it. Manipulate to test (for example) that wonky b-vectors can be detected, that it works with an odd...
Basically wrap the ungodly docker command that you would have run so that all you would have to do is something like: dmriprep_docker $BIDS_FOLDER
Per conversation with @akeshavan, I'm putting this here for some measure of posterity. Right now smriprep/fmriprep does not handle preprocessed Freesurfer for longitudinal data (using the Freesurfer longitudinal recon-all pipeline)....
I'm relatively new to dwi preprocessing. Would adding the following steps (added the mrtrix commands) as optional steps before eddy be useful? - denoising (`dwidenoise`) - unringing (`mrdegibbs`) - upsampling...
We need two pipelines: one with FSL eddy and one with FLIRT. FSL eddy is preferred so the CLI should determine whether the input dataset meets the requirements for eddy....
I think that typically an s3 bucket would have just one study organized as BIDS within it.
Package up Freesurfer to run with Cloudknot/AWS. I already have the code here: https://github.com/uw-biomedical-ml/mri2mri_notebooks/blob/master/ck-freesurfer-segmentations.ipynb
for some odd reason `img.get_fdata` kills my python kernel, but the deprecated `get_data` does not. I'm not sure how to debug this because everything just dies!