fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
Bug fix release in the 23.2.x series.
Masks, BOLD references and T2* maps resampled into template spaces had their order of transforms inverted. BOLD files were unaffected.
This release also preserves the TR in the NIfTI header of BOLD series.
init_ds_volumes_wf (https://github.com/nipreps/fmriprep/pull/3238)Full Changelog: https://github.com/nipreps/fmriprep/compare/23.2.0...23.2.1
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. To disable Jacobian weighting, use --ignore fmap-jacobian.
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.
github_link.py (#3144)Full Changelog: https://github.com/nipreps/fmriprep/compare/23.1.4...23.2.0
The final alpha release of fMRIPrep 23.2.0.
With thanks to everybody who has reported bugs and shared data for testing.
Full Changelog: https://github.com/nipreps/fmriprep/compare/23.2.0a2...23.2.0a3
A quick turnaround patch for the 23.2.0a pre-releases. Thanks to @smeisler for spotting a bug. This release includes the necessary fix in sMRIPrep, as well as several improvements to tests and opportunistic cleanups.
github_link.py by @DimitriPapadopoulos in https://github.com/nipreps/fmriprep/pull/3144
Full Changelog: https://github.com/nipreps/fmriprep/compare/23.2.0a1...23.2.0a2
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.
Patch release in the 23.1.x series.
This release prioritizes single-band reference BOLD images during SyN-SDC schemes. Additionally, an indices inconsistency was fixed for CIFTI volumetric data.
Bug fix release in the 23.1.x series.
In rare cases where Freesurfer is unable to align to its default atlas in Talairach registration, it was unable to fall back to the Schwartz atlas because we were not including it in the Docker image. This release exists to provide an updated Docker image, and no upgrade is needed for users not encountering this issue.
Full Changelog: https://github.com/nipreps/fmriprep/compare/23.1.2...23.1.3
Bug fix release in the 23.1.x series.
This release correctly generates *_space-fsLR_desc-reg_sphere.surf.gii, which was previously a copy of the standard *_desc-reg_sphere.surf.gii. Additionally, warnings are now correctly emitted when AROMA-related CLI options are used.
Full Changelog: https://github.com/nipreps/fmriprep/compare/23.1.1...23.1.2
Bug fix release in the 23.1.x series.
This release corrects a small error that prevented the "goodvoxels" mask from being placed in the output directory if no FreeSurfer output spaces were specified.
Full Changelog: https://github.com/nipreps/fmriprep/compare/23.1.0...23.1.1
New feature release in the 23.1.x series.
This release substantially reworks the resampling to fsLR grayordinate space, better accounting for partial volumes and high variance voxels. If you are resampling using --project-goodvoxels, we strongly recommend upgrading.
Fieldmap handling is improved, with better preference given to single-band references in both PEPolar and SyN-SDC schemes. Additionally, fMRIPrep will no longer estimate fieldmaps that are not intended to be used to correct BOLD series, reducing unneeded processing.
This release removes ICA-AROMA from the fMRIPrep workflow. To use ICA-AROMA, set MNI152NLin6Asym:res-2 as a target output space. MELODIC and ICA-AROMA can be run on the resulting images in a separate pipeline. For further information on the reasoning behind this change, see GitHub issue #2936.
This release increments the versions of ANTs and FSL bundled in the Docker image.
With thanks to Eilidh MacNicol, Basille Pinsard and Taylor Salo for contributions in fMRIPrep and SDCflows.
--me-t2s-fit-method parameter (#3030)Full Changelog: https://github.com/nipreps/fmriprep/compare/23.0.2...23.1.0