Fix phase encoding handling on 3.0.7 #3146
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This reverts commit 38910df.
- renamed phaseencoding.save() to phaseencoding.save_table() to disambiguate from FSL topup format. - dwifslpreproc: Do not attempt to write FSL eddy format phase encoding data from a piped image; force write of a NIfTI image here, even if it is somewhat redundant. - Docs: More description on ambiguity between phase encoding "table" and FSL topup format phase encoding file.
- On inability to merge diffusion gradient tables, issue message at info level rather than warning. - Suppress warning message on inability to modify phase encoding ifnromation to match image realignment tinformation only occur if such phase encoding information is both present and otherwise not explicitly flagged as being no longer valid. - For import / export of phase encoding information in external metadata files alongside different image formats, issue warning-level messages rather than exceptions, and do so across the full spectrum of potentially erroneous usages. - Docs: Full section in phase encoding handling page on the distinction between "table" and "topup" formats.
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.
With up-to-date FSL, it appears that not only "standard_space_roi" depends on Unix command "dc", but also "bet".
Lestropie
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Aug 13, 2025
Tests observed to fail on MacOS in #3146.
Lestropie
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Aug 13, 2025
Tests observed to fail on MacOS in #3146.
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Ready for review. Have checked test logs for erroneous error messages. Python command tests pass with the exception of some |
bjeurissen
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Tested on the workshop single-subject data and appears to fix the issue.
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Initial work on resolving #3142. Committing to GitHub so that I can run testing on another system.
dwifslpreproctests (which don't get run as part of CI) pass.dwifslpreprocand everything else) for any excess of warning messages.