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0.13.0

0.12.2 (November 7, 2020)

Adds options for processing infant dMRI data. Also enables running without a T1w image.

  • Adds --dwi-only and --infant options to QSIPrep. (#177)

0.11.0 (August 12, 2020)

NEW: Workflow defaults have changed. T1w-based spatial normalization is done by default (disabled by --skip-t1-based-spatial-normalization) and dwi scans are merged before motion correction by default (disabled by --separate-all-dwis).

  • Deprecate some commandline arguments, change defaults (#168)
  • Fix typo in workflow names (#162)
  • Fix bug from 0.10.0 where ODFs were not appearing in plots (#160)

0.10.0 (August 4, 2020)

  • Adds support for oblique acquisitions (#156)

0.9.0beta1 (June 17, 2020)

  • Adds support for HCP lifespan sequences
  • Introduces --distortion-group-merge option for combining paired scans

0.8.0 (February 12, 2020)

  • Removes oblique angles from T1w headers to fix N4 bug (#103)

0.7.2 (February 4, 2020)

  • Fixed a bug in b=0 masking when images have high signal intensity in ventricles (#99)

0.7.1 (January 29, 2020)

  • Image QC summary data is produced for each output (#95)
  • Update DSI Studio (#88)
  • Update ANTs (#80)
  • Include workflows for ss3t (#82)
  • Add some boilerplate to the FSL workflow (#38)
  • Reduce the number of calls to N4 (#74, #89)
  • Add CUDA capability in the containers (#75)
  • Add mrdegibbs and accompanying reports (#58)
  • Fix reports graphics (#64)
  • Rework the DWI grouping algorithm (#92)

0.6.7 (January 9 2020)

This release adds some rather big updates to QSIPrep.
  • FSL is updated to version 6.0.3
  • CUDA v9.1 support is added to the image (works with GPUS in Docker and Singularity)
  • A new robust b=0 masking algorith is introduced.

0.6.5 (Nov 21, 2019)

  • Improved handling of Freesurfer path (#50)
  • Better logic in commandline argument checking (#50, #62)
  • More robust brain masking for b=0 reference images (#73)
  • Bugfix for reverse phase encoding directon dwi series (#68)
  • Bugfix for warping eddy's CNR output (#72)

0.6.4, 0.6.4-1 (Nov 11, 2019)

  • IMPORTANT: commandline call changed to use official BIDS App
  • eddy will use multiple cores if available
  • Fixed bug in sentry interaction

0.6.2, 0.6.3RC1, 0.6.3RC2 (October 27, 2019)

  • Bugfix: masking was not working on eddy.
  • Bugfix: static versioning was not workign in the container.
  • New graphics in the documentation.
  • Use BSpline Interpolation if --output-resolution is higher than the input resolution.

0.6.0RC1, 0.6.2 (October 13, 2019)

An issue was discovered in how voxel orientation interacts with TOPUP/eddy and outside fieldmaps. Unless everything is in LAS+ prior to going into TOPUP/eddy, the warps are incorrectly applied at the end of eddy. This resulted in fieldmap unwarping reports that looked good but a final output that is bizarrely warped. Additionally, GRE fieldmaps would result in outputs being under-unwarped. To fix all of these, TOPUP (if PEPOLAR fieldmaps are being used) and eddy occur in LAS+, then their outputs are converted to LPS+ for GRE fieldmaps, SyN. The rest of the pipeline happens in LPS+, like the SHORELine version.

  • Update installation method to match fMRIPrep
  • Add CI tests for reconstruction workflows
  • Make the --sloppy option affect the reconstruction workflows
  • Fixes bug in 3dSHORE reconstruction (incorrect scaling)
  • CRITICAL bug fix: convert everything to LAS+ if eddy is going to be used
  • Added built-in reconstruction workflows
  • Added Brainnetome, AICHA and the remaining Schaefer atlases

0.5.1, 0.5.1a, 0.5.2 (September 10, 2019)

  • Address issues in Nipype causing random crashes

0.5.0 (August 11, 2019)

  • Use antsMultiVariateTemplateConstruction2.sh to make a b=0 template across scan groups
  • Control the number of template iterations and deformation model with --intramodal_template_iters and --intramodal_template_transform.

0.4.6 (July 23, 2019)

  • More documentation updates
  • MSD calculated for MAPMRI

0.4.5 (July 22, 2019)

  • Scalar outputs from MAPMRI

0.4.4 (July 19, 2019)

  • Default eddy configuation changed to not use CUDA by default.
  • Valerie added content to documentation

0.4.3 (July 18, 2019)

FSL tools are used to match SHORELine motion parameters to those from eddy.

  • Fieldcoefs are calculated from PEPOLAR and GRE fieldmaps and sent to TOPUP
  • Motion estimates from SHORELine match eddy

0.4.0 (June 7, 2019)

Add workflows for eddy and TOPUP.

  • Adds eddy tests on CircleCI.