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- 5 commits
- 29 files changed
- 5 contributors
Commits on Mar 25, 2025
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Add
smoothingandotsu_thresholdautotrack arguments (#219)* add smoothing and otsu_threshold to dsistudio autotrack * Add smoothing and otsu to dsi_studio.py argstring Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu> * finish linting interfaces/dsi_studio.py --------- Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>
Commits on Mar 26, 2025
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Allow desc entity in recon scalar derivatives (#220)
* Try raising on desc issue. * Update dipy.py * Update recon_scalars.py * Fix? * Update recon_scalars.py * Revert new desc entity.
Commits on Apr 3, 2025
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Tissue fraction modulated ICVF and OD maps (#218)
* Add AMICO modulated maps and RMSE to output - AMICO produces ICVF and OD maps modulated by the non isotropic tissue fraction. This makes these available. - AMICO also produces (N)RMSE maps of the observed vs predicted signal. Saving these enables QC and other assessments of parameter selection. * Add outputs to NODDI output spec * Make sure modulated files are available for FIBGZ * fix typo * still fixing * Update converters.py * Fix report documentation. * Update amico_noddi.yaml Change naming structure so that "desc" isn't used. * fix reports * last report typos * Now final typo * fix formatting issues * Other whitespace * Update amico_noddi.csv * Hopefully final linting errors * Update builtin_workflows.rst Adds reference to Parker for use of tissue fraction modulated outputs. * Updates to use desc field * Update qsirecon/workflows/recon/amico.py Co-authored-by: Taylor Salo <tsalo90@gmail.com> * Fix tests * Make linter happy * calculate tissue fraction * tf in expected outputs * json + lint --------- Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu> Co-authored-by: Taylor Salo <tsalo90@gmail.com> Co-authored-by: Matt Cieslak <mattcieslak@gmail.com>
4 people authoredApr 3, 2025
Commits on Apr 10, 2025
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Calculate kurtosis microstructure scalars with new `DKI_reconstructio…
…n` parameter (#223) * Add new DIPYDKI metrics. * Update expected outputs. * Try fixing. * Fix! * Update dipy.py * Fix. * Only get microstructure metrics if not sloppy. * Drop new expected outputs. * Change model of microstructural metrics. * Update. * Split DKI nodes. * Add new scalars. * Drop ga. * Update dipy.py * Enable wmti just to test. * Revert "Enable wmti just to test." This reverts commit 3b70b5d. * Add dkimicro kfa scalar.
Commits on Apr 14, 2025
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