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MASILab / Synb0-DISCO

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps
https://my.vanderbilt.edu/masi
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What should go into argument_list variable? #1

Closed josephmje closed 5 years ago

josephmje commented 5 years ago

Hi,

I'm trying to set up this package in my lab. I was confused about what should go in the <argument_list> when running run_synb0_run.sh. Is there any documentation for this?

Thanks

hanscol commented 5 years ago

I apologize for the lack of a readme, this work was always intended to be a docker which you can currently find at hansencb/synb0-disco on docker hub. run_synb0_run.sh expects a path to a matlab compiler runtime for 2018a. It also expects a file /INPUTS/T1.nii.gz and a directory /OUTPUTS to exist, which makes more sense in the docker. I would suggest visiting the docker hub page and see if that clears anything up.

josephmje commented 5 years ago

Thank you @hanscol ! Would you happen to have the Dockerfile used to create the container as well? I think the docker is missing FSL.

hanscol commented 5 years ago

I've attached the docker file, though the Matlab runtime file and the fsl build are not included in this repository. I think there is a bug in the docker that tries to source the fsl path within the script, but the dockerfile adds it to the path correctly and fsl was copied to the docker.

Dockerfile.txt

josephmje commented 5 years ago

Ahhh k. Thank you! I was confused about the FSL warnings after running the docker but the output seems to be ok.