Faster quasiraw pipeline + mask interpolation fix - #60
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+ use a 2mm space to speed the process. |
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+ add T2w and FLAIR support. |
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This PR:
Fixed mask interpolation (quasiraw.py:175)
The quasiraw pipeline scales the brain mask alongside the anatomical image (interfaces.scale). Previously both calls used FSL flirt's default trilinear interpolation, which produces non-binary values when applied to a binary mask. The mask scaling call now explicitly passes interp="nearestneighbour" so mask voxels stay binary after resampling.
Added interp parameter to scale() (fsl.py:201-224)
New optional parameter forwarded to flirt -interp, defaulting to None (flirt's own default, trilinear) — needed to support the fix above without hardcoding it for every caller.
Speed optimizations in affine() and biasfield() (fsl.py:305-56, ants.py:74)
affine(): restricts the flirt rotation search range to ±30° on all three axes (-searchrx/ry/rz -30 30) instead of FSL's much wider default, cutting registration search time.
biasfield(): increases N4BiasFieldCorrection's shrink factor (-s) from 1 to 4, which downsamples the image before estimating the bias field — a common speed/accuracy tradeoff for large-scale batch processing.
Together these make the quasiraw preprocessing step noticeably faster for batch runs while correcting a real bug (binary mask corruption from trilinear resampling).