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Fix fastsurfer option for T1 surface reconstruction + Add key QC steps in MultiQC report. #6

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merged 52 commits into from
Jan 6, 2025

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@gagnonanthony gagnonanthony commented Dec 6, 2024

The existing fastsurfer modules were missing the computation of a transform file required for atlas mapping. Also, I reduced the container size for atlases and added more tests.

Integrated QC screenshots to the MultiQC report per subject:

  • Tissue segmentation overlaid on a T1.
  • Labels overlaid on anat.
  • Shell distribution.
  • Metrics screenshot.
  • Tracking mask overlaid on TDI map.

Added a population-level MultiQC report including quantitative assessment of processing quality:

  • DICE score between TDI mask and tracking mask.
  • Streamline counts.
  • Volume, thickness, and surface area of cortical and subcortical parcels.

#7

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@gagnonanthony gagnonanthony self-assigned this Dec 6, 2024
@gagnonanthony gagnonanthony changed the title Fix fastsurfer option for T1 surface reconstruction Fix fastsurfer option for T1 surface reconstruction + Add key QC steps in MutliQC report. Dec 20, 2024
@gagnonanthony gagnonanthony added the enhancement New feature or request label Dec 20, 2024
@gagnonanthony gagnonanthony changed the title Fix fastsurfer option for T1 surface reconstruction + Add key QC steps in MutliQC report. Fix fastsurfer option for T1 surface reconstruction + Add key QC steps in MultiQC report. Jan 6, 2025
@gagnonanthony gagnonanthony merged commit e689d05 into scilus:main Jan 6, 2025
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