What’s new

0.6.0

This release makes substantial changes to ASLPrep. The two main changes are (1) the Schaefer atlases are replaced with the PennLINC team’s new 4S atlases, which combine the Schaefer cortical atlases and several subcortical atlases, and (2) a major rearchitect of the package based on fMRIPrep version 23.2.0a2. The latter allows ASLPrep to run FreeSurfer reconstruction, write out CIFTI and GIFTI format derivatives, and correctly apply susceptibility distortion correction with SDCFlows (although SDC support is dependent on the next SDCFlows release, so in practice it won’t work just yet).

I’d like to credit Chris Markiewicz (@effigies) for doing the majority of the work in the fMRIPrep refactor, which I was able to copy and adapt for ASLPrep.

Here’s a list of parameter changes with this release:

  • Users must point to the actual output directory. aslprep will no longer be appended automatically.

  • The parameter --anat-derivatives is replaced with --derivatives, which takes one or more paths to sMRIPrep or ASLPrep derivatives.

  • The parameter --dummy-vols is now --dummy-scans to match fMRIPrep.

  • The following parameters are newly added: --bids-database-dir, --level, --medial-surface-nan, --project-goodvoxels, --cifti-output, --no-msm, --no-submm-recon, --fs-subjects-dir, --fs-no-reconall, and --config-file.

Output changes:

  • The native-space aslref image is now split into desc-hmc and desc-coreg versions.

  • desc-pvGM_cbf is renamed to desc-basilGM_cbf.

  • desc-pvWM_cbf is renamed to desc-basilWM_cbf.

  • desc-confounds_regressors.tsv is renamed to desc-confounds_timeseries.tsv.

  • The transform from-T1w_to-scanner_mode-image_xfm.txt is no longer generated. The inverse is invertible, so the information is still available.

  • The transform from-scanner_to-T1w_mode-image_xfm.txt is split into from-orig_to-aslref_mode-image_xfm.txt and from-aslref_to-T1w_mode-image_xfm.txt files.

πŸ›  Breaking Changes

πŸŽ‰ Exciting New Features

πŸ› Bug Fixes

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.5.1…0.6.0

0.5.1

πŸ› Bug Fixes

Other Changes

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.5.0…0.5.1

0.5.0

πŸŽ‰ Exciting New Features

πŸ› Bug Fixes

Other Changes

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.4.0…0.5.0

0.4.0

This release re-implements multi-delay PCASL and single-delay Q2TIPS PASL support.

Additionally, we have replaced certain BOLD-specific steps with ASL-compatible alternatives. One such case is slice timing correction. Rather than interpolate the ASL time series to perform slice timing correction (as in BOLD preprocessing), ASLPrep now shifts PLDs according to the slice timing. The other major change is to motion correction, which is now performed separately for each image type in the ASL time series (e.g., control, label, and M0 volumes).

Thanks to Sudipto Dolui, Jian Hu, Jan Petr, Manuel Taso, and Kay Jann for their help and feedback.

πŸ›  Breaking Changes

πŸŽ‰ Exciting New Features

πŸ› Bug Fixes

Other Changes

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.3.0…0.4.0

0.3.0

0.3.0 reflects renewed maintenance for ASLPrep.

The primary focuses of this release are: (1) fixing easily-fixable bugs, (2) disabling broken features with difficult-to-fix bugs, (3) cleaning up the codebase, (4) expanding test coverage, and (5) ensuring that outputs are BIDS-compliant.

To that end, we have unfortunately had to temporarily drop support for multi-PostLabelingDelay data, as well as PASL data with the Q2TIPS BolusCutOffTechnique. We will work on fixing these features for the next release.

Additionally, this release includes a number of breaking changes. We have renamed several of the outputs to ensure that they are BIDS-compliant. These outputs may need to change again in the future, but that will happen in the next minor release (0.4.0) at the earliest. See the table below for a list of the changed filenames.

Description

<0.3.0

0.3.0

CBF time series

_cbf.nii.gz

_desc-timeseries_cbf.nii.gz

Mean CBF

_mean_cbf.nii.gz

_cbf.nii.gz

CBF time series after SCORE denoising

_desc-score_cbf.nii.gz

_desc-scoreTimeseries_cbf.nii.gz

Mean CBF after SCORE denoising

_desc-score_mean_cbf.nii.gz

_desc-score_cbf.nii.gz

Bolus arrival time/arterial transit time

_desc-bat_cbf.nii.gz

_att.nii.gz

Additionally, we have changed the atlases that are used for the parcellated CBF files. We have brought the atlases in line with those used by XCP-D. However, in the near future, we plan to update these atlases again, so that they are synchronized across ASLPrep, XCP-D, and QSIPrep, so please be aware of that upcoming change.

πŸ›  Breaking Changes

πŸŽ‰ Exciting New Features

πŸ› Bug Fixes

Other Changes

New Contributors

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.2.8…0.3.0

0.2.7

Bids validation

0.2.6

11/12/2020

ENH - Add GE SCAN processing with deltam or cbf

ENH - supressed freesurfer processing, FSL FLIRT with BBR for registration

ENH - basil and scorescrub as options, cbf computation is only default