0.18.0alpha0

First release moving towards 1.0! Please open bug reports if anything suspicious comes up.

What's Changed

• Bump sentry-sdk from 0.13.1 to 1.14.0 by @dependabot in #539
• [ENH] Update FreeSurfer to 7.3.1, dmri-amico to 1.5.4 by @mattcieslak in #537
• WIP: ENH: Make pyAFQ tests faster, add export all by @36000 in #534
• [ENH] move biascorrect so it runs on resampled data by default by @mattcieslak in #527
• [Fix] Fix threading on DRBUDDI interface by @mattcieslak in #540
• [ENH] add CNR to the imageqc.csv by @mattcieslak in #541
• [FIX] pin pandas version to < 2.0.0 by @mattcieslak in #543
• ENH: Replace avscale with non-fsl tools by @jbh1091 in #542
• ENH: Replace fsl applymask by @jbh1091 in #544
• Replace fsl split by @jbh1091 in #548
• [FIX] Update distortion_group_merge.py by @smeisler in #555
• [ENH] Redo anatomical workflow by @mattcieslak in #553
• [FIX] remove pre bids-filter acq type argument by @octomike in #557
• FIX: Replace deprecated np.int instances by @smeisler in #558
• [WIP] ENH: 482 remove fsl dependency by @jbh1091 in #498
• [ENH] Update TORTOISE for improved T2w registration by @mattcieslak in #564
• [FIX] T2w anat-modality issues by @mattcieslak in #565
• [FIX] update boost in tortoise by @mattcieslak in #569
• [FIX] connections on multi-anat workflow by @mattcieslak in #572
• [ENH] Update DSI Studio to the latest commit by @mattcieslak in #573
• [ENH] Add DSI Studio AutoTrack recon workflow by @mattcieslak in #576

New Contributors

• @dependabot made their first contribution in #539
• @jbh1091 made their first contribution in #542
• @smeisler made their first contribution in #555

Full Changelog: 0.17.0...0.18.0alpha0

0.16.1

What's Changed (including over the release candidates)

• [ENH] Add pyafq by @36000 in #398
• [FIX] Add atlases back into derivatives by @mattcieslak in #418
• [ENH] Add exemplar streamlines to mrtrix connectivity workflows by @mattcieslak in #420
• [ENH] Use updated atlases by @mattcieslak in #426
• [FIX] schaefer400 atlas by @mattcieslak in #428
• [ENH] optimize connectome2tck by @mattcieslak in #429
• Update citing.rst by @hamsiradhakrishnan in #430
• [FIX] use safe_load instead of load by @mattcieslak in #443
• [ENH] update itk to 5.3 by @mattcieslak in #449
• [FIX] Add back fugue and prelude to the qsiprep image by @mattcieslak in #463
• [ENH] Add option for using raw images for SDC by @mattcieslak in #465

New Contributors

• @36000 made their first contribution in #398
• @hamsiradhakrishnan made their first contribution in #430

Full Changelog: 0.15.4...0.16.1

0.16.0RC3

MAJOR UPDATES AND BUGFIXES: We do not recommend using 0.15 for reconstruction workflows.

Most notably PyAFQ is available as a reconstruction workflow. The default atlases included in
QSIPrep have been updated to include subcortical regions if they weren't already present in the
original atlas. We've also added connectome2tck so that you can check your connectivity
matrices in mrview's connectome viewer.

• Adds multithreading to connectome2tck #429
• Fixes a naming error in the schaefer 400 atlas #428
• Add PyAFQ reconstruction workflows #398 Credit: @36000
• Make sure all recon workflows respect omp_nthreads #368
• Add DKI derivatives #371
• Properly transform 4D CNR images from Eddy #393
• Update amico to version 22.4.1 #394
• Fix concatenation bug #403 credit: @cookpa
• Prevent divide by zero error #405 credit: @cookpa
• Critical Fix, use correct transform to get atlases into T1w space #417
• Add resampled atlases back into derivatives #418
• Add connectome2tck exemplar streamlines for mrtrix connectivity workflows #420
• Update the atlases to include subcortical regions #426 details here

0.15.1: DEPRECATED

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
   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)

0.14.3

Updates parameters for Patch2Self denoising

0.14.2

Bugfixes and documentation

• Updates documentation for containers (#270)
• Fixes a bug when reading fieldmap metadata from datalad inputs (#271)
• Change incorrect option in the documentation (#272)

0.14.0

Adds a new reconstruction workflow for the NODDI model.

• Adds NODDI reconstruction workflow (#257). Thanks @cookpa!
• Fixes issue with unequal aspect ratios in q-space plots (#266)

0.13.1

• Adds a flag for a BIDS filter file #256
• Fixes a bug where --dwi-only is selected along with --intramodal-template #254

0.13.0

Many bugfixes

• Fix bug that produced flipped scalar images (#251)
• Added a default working directory to prevent uninterpretable error message (#250)
• Fix a bug in the dipy_3dshore reconstruction workflow (#249)
• Remove hardlinking from DSI Studio interfaces (#214)
• Add an option to use a BIDS database directory (#247)
• Fix bug in interactive reports for HCP-style acquisitions (#238)
• Update defaults for Patch2Self (#230, #239)
• Remove cmake installer from docker image after compiling ANTS (#229)

0.13.0RC2

• Fixes an issue with creating interactive reports when using a distortion group merge. #232
• Changes defaults for patch2self #239