added rule to summarize surf metrics over subfields #178
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simple version for non-contributors
- adds a reg_t2_to_template rule
- adds T2w CITI168 template image for this rule
- adds a --reg_t2_to_template CLI option to enable this rule (otherwise
default behaviour is to use T1w as usual)
- add a {native_modality} wildcard so rules that register or resample to
cropT1w/T1w space are now generic
- adds cropT2w to possible output_spaces
- in order to run T2w-only workflow, just need to specify:
`--reg_t2_to_template --output_spaces cropT2w`
- working with dry-run, and some initial testing on HSG data
- TODO: test entire workflow on real data
- TODO: make sure all dry-run testing works
- TODO: add more dry-run test cases
- TODO: update the documentation
Fixes error when multiple T2w images exist
patch for skip_templateshape
was 192x256x256, but this was cropping out some hippocampal tissue sometimes
- output_spaces now can be cropnative or corobl - made registration with the native modality the default (e.g. T2w used for registration if T2w workflow used), can be overriden with `--t1_reg_template`) - unrelated, removed `neonateT1w` modality choice, this is implemented through forcing the nnunet model instead and shouldn't have been added there in the first place (can later try to implement as a modality)
- output_spaces now only used as an option to specify an *additional* output space, specifically to specify T1w as an output space when modality==T2w. Otherwise all results will be registered to T2w images, which may not always be desired. Using `--output_space T1w` then adds cropT1w and T1w images to the outputs. - added a dry-run test for this
(i'm on browser so testing is harder)
the bounding box for Lhipp actually was Rhipp (and vice versa), so this swaps them. This only was affecting the `--modality hippdwi` workflow, thanks to Luciana for pointing this out!
Unfolddentatetemplate patch
* updates docs for multi atlases + addnl fixes * added dryrun test for multiple atlases * refactored the code from #200 a bit more - adding the atlas to the metrics list was hacky - went back to a separate rule for hipp/dentate spec files to allow subfields to be in one and not the other, so we can just expand over atlases instead - tested and has same functionality, but will be easier to maintain down the road * tiny typo fix Co-authored-by: jordandekraker <[email protected]>
* bugfix: subfield+tissue for new atlases, and tsv files Two related fixes: 1. New atlases were still using the bigbrain dseg.tsv for generating the subfield volumes.tsv files. These have now been added. 2. The way the postproc tissue labels (dg, srlm, cyst) were being added to the subfields was also hardcoded for the bigbrain atlas. Have now added a section in the config file to customize what labels these map to, so that e.g. the dentate gyrus is merged into the existing label number, and that the SRLM/Cyst labels do not conflict with the labels, and are maximal (so they override the others). Previously the magdeburg subiculum label (8) was same as cyst, so these became merged.
bringing in latest changes to get workflow working again
- had some conflicts to resolve from the atlas PRs - working with dry-run now - TODO: full test, and consider making surf metrics consistent with volume tsv files in format/layout -- or maybe an additional single tidy table for all
however the cifti-parcellate approach with custom csv header isn't great when we have custom atlases -- instead should just make a script that reads in the label.gii, metric.gii, and labellist file and manually create the dataframe (output to tsv).
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To do: