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nipreps / smriprep

Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
https://nipreps.github.io/smriprep
Apache License 2.0
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More forgiving FreeSurfer check #226

Open effigies opened 4 years ago

effigies commented 4 years ago

Currently, we use Nipype's full recon-all interface to detect whether FreeSurfer has been fully run, and also to finish the run if it has not.

This has complications when using FreeSurfer subjects reconstructed with different versions, as well as FastSurfer. Instead, it may make sense to directly detect the outputs we need, and only construct the recon-all workflow if they are not all available.

Ref. https://github.com/Deep-MI/FastSurfer/issues/21

m-reuter commented 2 years ago

Also double check what outputs you really need. For example the T1.mgz should not be needed for anything as it is an intermediate file. If you only need the header for mapping across FS conform space and the original input, then use e.g. orig.mgz instead.