What’s new

0.14.3 (September 16, 2021)

Change in behavior in Patch2Self:

  • Updates Patch2Self with optimal parameters (use OLS instead of ridge)

0.14.2 (July 11, 2021)

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 (July 2, 2021)

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 (June 14, 2021)

  • Adds a flag for a BIDS filter file #256

  • Fixes a bug where –dwi-only is selected along with –intramodal-template

0.13.0 (May 5, 2021)

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)

0.13.0RC1 (January 19, 2021)

This version introduces major changes to the TOPUP/eddy workflow. Feedback would be greatly appreciated!

  • Added new algorithm for selecting b=0 images for distortion corretion (#202)

  • Added the Patch2Self denoising method (#203, credit to @ShreyasFadnavis)

  • Documentation has been expanded significantly (#212)

  • Boilerplate for DWI preprocessing is greatly expanded (#200)

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.