FIX: Do not reorient magnitude images #98
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@oesteban Because this is so small, I'm going to put on my release manager hat and merge to start the process to get fMRIPrep 1.5.10 out the door. Please interrupt if you have concerns. |
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1.0.6 (April 15, 2020) Bug-fix release. * FIX: Do not reorient magnitude images (#98)
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1.5.10 (April 16, 2020) Bug-fix release in the 1.5.x series. This release fixes a bug for **phase-difference fieldmaps that are not in RAS+ orientation**. The bug presented as an error if the orientation was reordered relative to RAS+ (for example, AIL+) and the swapped dimensions were not of the same size. Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle if the original orientation was LAS+. Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not currently considered problematic. This bug affects all previous versions of fMRIPrep, as well as versions 20.0.0-20.0.5. * FIX: Do not reorient magnitude images (nipreps/sdcflows#98)
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20.0.6 (April 16, 2020) Bug-fix release in the 20.0.x series. This release fixes a bug for **phase-difference fieldmaps that are not in RAS+ orientation**. The bug presented as an error if the orientation was reordered relative to RAS+ (for example, AIL+) and the swapped dimensions were not of the same size. Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle if the original orientation was LAS+. Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not currently considered problematic. This bug affects all earlier versions of fMRIPrep, except for 1.5.10 and any future releases in the 1.5.x series. * FIX: Do not reorient magnitude images nipreps/sdcflows#98
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In #33 it is shown that fieldmaps in AIL orientation produce an error in
sdc_estimate_wf.phdiff_wf.fmap_postproc_wf.cleanup_wf.Despikewhere the brainmask generated insdc_estimate_wf.phdiff_wf.magnitude_wf.betis in a different orientation.This is because the input to BET is reoriented to RAS in the
magmrgstep. I considered forcing all images to RAS, but that has the potential to cause problems withPhaseEncodingDirection, which is one of the voxel dimensionsi,j, andk, and not coded in RAS space.The simpler solution is simply not to reorient images during this workflow, to ensure that calculations are performed as intended. A further validation step could ensure that all fieldmap images have the same orientation and voxel sizes, but that would be a more significant change.
Because this is a change to an interface input, workflow directories can be reused without clearing. This can be safely included in the 1.5.x series of fMRIPrep.
Fixes #33.