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bids-apps / freesurfer

BIDS app wrapping recon-all from FreeSurfer
Apache License 2.0
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-3T flag option #42

Closed niniko1997 closed 6 years ago

niniko1997 commented 6 years ago

recon-all for freesurfer has a -3T flag (https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags) that you can pass to the command. It enables freesurfer to do intensity corrections that create more accurate segmentations for 3T scans.

I've added the option to pass in [--3T {true, false}] to the docker image (default is true). If true, recon-all will run with the -3T flag added to the command.

niniko1997 commented 6 years ago

Brilliant idea. -3T is now conditionally added to input_args

chrisgorgo commented 6 years ago

Thank you for your contribution!