Release notes
New feature release in the 23.2.x series.
This release wraps up a significant refactor of fMRIPrep. The main new features can be used with the --level and --derivatives flags.
The --level flag can take the arguments minimal, resampling or full. The default is full, which should produce nearly the same results as previous versions. minimal will produce only the minimum necessary to deterministically generate the remaining derivatives. resampling will produce some additional derivatives, intended to simplify resampling with other tools.
The --derivatives flag takes arguments of the form name=/path/to/dir, for example --derivatives anat=$SMRIPREP_DIR. If provided, fMRIPrep will read the specified directories for pre-computed derivatives. If a derivative is found, it will be used instead of computing it from scratch. If a derivative is not found, fMRIPrep will compute it and proceed as usual.
Taken together, these features can allow a dataset provider to run a minimal fMRIPrep run, targeting many output spaces, while a user can then run a --derivatives run to generate additional derivatives in only the output spaces they need. Another use case is to provide an precomputed derivative to override the default fMRIPrep behavior, enabling easier workarounds for bugs or experimentation with alternatives.
Additionally, this release includes a number of bug fixes and improvements. This release adds support for MSM-Sulc, improving the alignment of subject surfaces to the fsLR template. This process is enabled by default, but may be disabled with the --no-msm flag.
This release resolves a number of issues with fieldmaps inducing distortions during correction. Phase difference and direct fieldmaps are now masked correctly, preventing the overestimation of distortions outside the brain. Additionally, we now implement Jacobian weighting during unwarping, which corrects for compression and expansion effects on signal intensity.
Finally, a new resampling method has been added, to better account for susceptibility distortion and motion in a single shot resampling to a volumetric target space. We anticipate extending this to surface targets in the future.
Changes
- FIX: Final revisions for next branch (#3134)
- FIX: Minor fixes to work with MSMSulc-enabled smriprep-next (#3098)
- FIX: Connect EPI-to-fieldmap transform (#3099)
- FIX: Use Py2-compatible version file template for fmriprep-docker (#3101)
- FIX: Update connections to unwarp_wf, convert ITK transforms to text (#3077)
- ENH: Restore carpetplot and other final adjustments (#3131)
- ENH: Restore CIFTI-2 generation (#3129)
- ENH: Restore resampling to surface GIFTIs (#3126)
- ENH: Restore confound generation (#3120)
- ENH: Restore resampling BOLD to volumetric templates (#3121)
- ENH: Restore resampling to T1w target (#3116)
- ENH: Add MSMSulc (#3085)
- ENH: Add reporting workflow for BOLD fit (#3082)
- ENH: Generate anatomical derivatives useful for resampling (#3081)
- RF: Write out anatomical template derivatives (#3136)
- RF: Update primary bold workflow to incorporate single shot resampling (#3114)
- RF: Update derivative cache spec, calculate per-BOLD, reuse boldref2fmap (#3078)
- RF: Split fMRIPrep into fit and derivatives workflows (#2913)
- DOC: Fix documentation and description for init_bold_grayords_wf (#3051)
- STY: Fix flake8 warnings (#3044)
- STY: Apply pyupgrade suggestions (#3043)
- MNT: Bump environment (#3132)
- MNT: Bump version requirements (#3107)
- MNT: http:// → https:// (#3097)
- MNT: Remove mritotal and dependencies from FreeSurfer ignore file (#3090)
- MNT: Update environment (#3073)
- MNT: Depend on newer sphinx (#3067)
- MNT: Install ANTs from conda-forge (#3061)
- MNT: Drop Python 3.8 and numpy 1.21 support (NEP29) (#3052)
- MNT: update update_zenodo.py script (#3042)
- MNT: Fix welcome message formatting and instructions (#3039)
- MNT: Python 3.11 should be supported (#3038)
- CI: Stop testing legacy layout (#3079)
- CI: Improve tag detection for docker builds (#3066)
- CI: Clean up pre-release builds (#3040)