ENH: Enable recon-all -FLAIR / -FLAIRpial options #2279
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| desc='Convert T2 image to orig directory') | ||
| use_T2 = traits.Bool(argstr="-T2pial", min_ver='5.3.0', | ||
| desc='Use converted T2 to refine the cortical surface') | ||
| FLAIR_file = File(exists=True, argstr="-FLAIR %s", |
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can we use a single input i.e. T2, perhaps with:
- a
requiresset foruse* - a description update saying T2 file can be T2 or FLAIR
?
freesurfer doesn't really distinguish between the inputs in the recon-all process, only the use options change some thresholds to fixing surfaces.
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When adding the images, -T2 <file> vs -FLAIR <file> dictates whether it's converted to orig/T2raw.mgz or orig/FLAIRraw.mgz Then -T2pial and -FLAIRpial draw from those files as well as set different options to mris_make_surfaces. (Also note that -T2 and -FLAIR are not mutually exclusive, but -T2pial and -FLAIRpial are.)
Also, recall that someone may use this in multiple stages. The -T2 <file> and -T2pial options may not be passed in the same interface, so dependencies between these options aren't necessarily going to be straightforward.
Given these considerations, do you see a way of simplifying this?
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@effigies - i was going to say we could set the appropriate argument in _format_arg. but since this interface offers the possibility of passing any of the Do* arguments, perhaps this is cleaner at this point. so i'm ok with the way this PR is currently implemented.
Codecov Report
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+ Coverage 72.52% 72.52% +<.01%
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Files 1188 1188
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Branches 8510 8510
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+ Hits 42892 42894 +2
Misses 14864 14864
Partials 1385 1385
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The invocation of the pial surface correction differs based on whether FreeSurfer thinks it's using a T2 or a FLAIR image. We should thus support both pathways.
Changes proposed in this pull request