dwifslpreproc: Fix for PE direction, but not readout time, in header#2722
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dwifslpreproc: Fix for PE direction, but not readout time, in header#2722
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If the phase encoding information present in the header is only the phase encoding direction, but not readout time is present, then the constructed phase encoding matrix will possess only three columns, not four. If this happens, but an attempt is then made to cross-reference the readout time in the phase encoding table generated from header content against what the user has specified at the command-line, then an unhandled exception will occur. This change prevents specifically the comparison of readout times from being made if no such information is present. Replacement for erroneous commit faf0788. Also includes additional test that results in an unhandled exception on 3.0.4 but executes successfully with this change.
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Fixed & added test as proof. Seeking approval review. |
daljit46
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Feb 5, 2025
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Because the section of code responsible for running FSL applytopupup now makes use of a temporary NIfTI image, diffusion and phase encoding data are absent. This resulted in failure of the subsequent dwi2mask call. Here the diffusion gradient table and other header key-value metadata are explicitly tracked for each individual volume group defined by phase encoding, so that they can be later suitably combined during image concatenation. Additionally fixes typo in dwifslpreproc test added in #2722.
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Error encountered by user attempting to process their own data during workshop.
Description in faf0788.