prepdwi for @kaitj ReproStudy

legacy release to tag the version used in the @kaitj ReproStudy manuscript submission

Move to semantic versioning, bugfixes

-bugfixes for custom mask handling
-move to semantic versioning
-note: this is a still a bugfix release, next bugfix release will be v0.0.14 and next minor release will be v0.1.0

Fixes for imported brain masks (beast/fmriprep)

Fixes bugs in handling imported brainmasks from beast/fmriprep

added correct_pd and option for preproc T1w from fmriprep

Updates:

• updated DTI fitting within DKE to use only shell 1
• added option for getting preproc T1w from fmriprep
• added --correct_pd option to enable path length correction in probtrackx

participant3 level analysis added

-added participant3 level analysis, for running connectivity on imported label maps (instead of performing internal niftyreg label propagation)

• see usage for more info
  -some fixes and refactoring for participant2 stage

fixed bug in checking for completion of gradcorr

-re-release for bug-fix that affected checking for completion of gradcorr step

fix symlinks and participant2

-fixes issues with symlinks
-copies atlas folder (instead of symlink) to fix broken participant2 analysis
-set number of threads to 1 for participant2
-remove bedpost log files
-add checks for dwi proc stages, exiting with 1 if a step fails

prepdwi for @DimuthuHemachandra PPMI study

legacy release to tag the version used in the @DimuthuHemachandra PPMI manuscript submission

participant2 features, dwi2mask, minor bugfix

Thanks @DimuthuHemachandra for new participant2 level features

New features:
-FA/MD-based connectivity matrices can now be produced with participant2 level analysis
-circleci testing for participant2 level analysis (with reduced dosenbach test atlas)
-dwi2mask for DWI brain masking instead of FSL (found to be more robust)

Bugfixes:

• DKE processing now re-enabled

Re-release for zenodo, to tag the version used in @DimuthuHemachandra manuscript submission

custom brainmask inputs

-custom brainmask (e.g. from BEaST pipeline) can be specified with --in_brainmask_dir
-bugfixes for atlas symlinks that caused issues with group-based analysis