A lot of changes in QSIPrep. The big-picture changes are
1. The build system was redone so a multistage build is used in a
different repository (https://github.com/PennLINC/qsiprep_build).
The container should be about half as big as the last release.
2. The way anatomical masks are handled in reconstruction workflows
has been changed so that FreeSurfer data can be incorporated.
3. FAST-based anatomically-constrained tractography is now deprecated in
QSIPrep. If you're going to use anatomical constraints, they should be
very accurate. The hybrid surface-volume segmentation (HSVS) is
*amazing* and should be considered the default way to use the
MRtrix3/3Tissue workflows. The
[documentation](https://qsiprep.readthedocs.io/en/latest/reconstruction.html)
describes the new built-in workflow names.
4. The reconstruction workflows have been totally refactored. This won't
affect the outputs of the reconstruction workflows, but will affect
anyone who is using intermediate files from the working directory.
The working directories no longer have those unfortunate `..`'s in
their names.
5. FSL is updated to 6.0.5.1!
Since these are a lot of changes, please be vigilant and check your results!
The QSIPrep preprocessing workflows have not changed with this release, but
the dependencies have been upgraded for almost everything.
* Update FSL to 6.0.5.1 (334)
* Move ODF plotting to a cli tool so xvfb is handled more robustly (357)
* Better FreeSurfer license documentation (355)
* Edited libQt5Core.so.5 so it's loadable in singularity on CentOS (336)
* Fixed typo in patch2self (338)
* Inaccurate bids-validator errors were removed (340)
* Bug in `--recon-input` fixed 286
* Correct streamline count is reported in the mrtrix connectivity matrices (330)
* Add option to ingress freesurfer data (287)
* Add Nature Methods citation to dataset_description.json
* Refactor build system (341)
* SHORELine bugfixes (301)
* Bugfix: handle cases where there is only one b=0 (279)