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More forgiving FreeSurfer check #226

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effigies opened this issue Aug 21, 2020 · 1 comment
Open

More forgiving FreeSurfer check #226

effigies opened this issue Aug 21, 2020 · 1 comment
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effort:medium Estimated medium effort task enhancement New feature or request impact:low Estimated low impact task

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@effigies
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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. Deep-MI/FastSurfer#21

@effigies effigies added enhancement New feature or request effort:medium Estimated medium effort task impact:low Estimated low impact task labels Aug 21, 2020
@m-reuter
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m-reuter commented Dec 1, 2021

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.

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Labels
effort:medium Estimated medium effort task enhancement New feature or request impact:low Estimated low impact task
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