v0.1.0

What's Changed

• Pin conda to 4.10.3 by @tkkuehn in #27
• remove out of date heuristic by @akhanf in #26
• Revamp dockerfile by @tkkuehn in #28
• Minor update to cfmm_base heuristic for T2 SPACe by @switt4
• Move to semantic versioning

New Contributors

• @tkkuehn made their first contribution in #27

Full Changelog: v0.0.6c...v0.1.0

adds UNI-DEN denoising factor command-line option

• exposes mp2rage denoising multiplicative factor to the CLI, default value of 6 works fine for 7T, but it seems >200 is needed for 3T

pin dcm2niix, more LOBE updates

-pins dcm2niix to latest release (was pinned to development branch before)
-more updates to LOBE heuristic and dealing with MEMPRAGE, combines echoes 1 and 2 (like HCP lifespan pipeline)

• UPDATE without typo in the tag

fix LOBE heuristic, move vNav files

• LOBE T1w heuristic needed fixing
• moved vNav intermediate files to subfolder of sourcedata instead of sourcedata

HCPLS, vNav, CS-GRE, ASPIRE

• fix meGRE corrector parse failure with GRE10
• fix real/imag swap bug
• added generation of phase images from real/imag (for GRE from bruker)
• handle fmap case2 (for philips sickkids data) (#15)
• vNav support, remove CogAtlasID, _scans.tsv, LOBE heuristic (#17)
• updated to HCPLS heuristics (#18)
• added compressed sensing GRE and ASPIRE to cfmm_base (#19)

multi-echo GRE and PD+T2 fixes

-fixes multi-echo GRE parsing that was broken during a v0.0.5f fix
-adds pd+t2 to possible names in series (before was just pd_t2)
-fixes PDT2 parsing for renaming to work more generally

bruker fixes and tar.gz

• made flair naming more permissive for 7T
• fix issue of non-ending mentions of GRE matching
• updates to cfmm_bruker, removed acq from dwi, and added T2 TurboRARE
• fixes for patientname parsing (related to Bruker data)
• handling tar.gz

bruker bmat/bvec/bval extraction

• enables extraction of Bruker B-matrix, bvec and bval data from Paravision metadata embedded in dicoms
• overrides .mvec file that is derived from b-matrix using dcm2niix

heuristic fix for dwi, bold_rest, and dealing with complex sa2rage

• fixed dwi specificity issue, will only grab DIFFUSION image_type now
• fixed similar problem in cfmm_bold_rest, now will not inadvertently pick up dwi
• removed sbrefs from fmap/dwi folders
• added correction scripts to deal with mag/phase sa2rage data (another post-upgrade fix)

fix b0-only bval/bvec, generate UNI-DEN T1w

• incorporates latest dcm2niix for adding bval/bvec for b0 only dwi data [*]
• added -x option to force dcm2niix direct nifti conversion into sourcedata folder
• added OGSE and uFA (experimental) to cfmm_base
• added tune-up script to generate a MP2RAGE UNI-DEN T1w file as long as UNI, INV1 and INV2 exist

[*] Note: this breaks bval/bvec generation for Bruker data -- as a fix, recommend to use the -x option and copy the resulting .mvec/bval files over from sourcedata to bids. TODO for dcm2niix: use Bruker metadata for extracting bvec/bval instead of Bmatrix..