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Labelmerge #30

Merged
merged 16 commits into from
Dec 5, 2022
Merged

Labelmerge #30

merged 16 commits into from
Dec 5, 2022

Commits on Dec 1, 2022

  1. add .gitignore

    @kaitj
    kaitj committed Dec 1, 2022
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  2. update resource files 

    - Added tpl and updated names for MNI152NLin6Asym
- Renamed MNI2009b -> MNI152NLin2009bAsym
- Removed unnecessary files
- Update config
    @kaitj
    kaitj committed Dec 1, 2022
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  3. update rule for removing thalamus labels from segmentation

    @kaitj
    kaitj committed Dec 1, 2022
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  4. Update tsv file for labelmerge 

    - Update config to include tsv for subcortical labels
    @kaitj
    kaitj committed Dec 1, 2022
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  5. Update config and fs tsv 

    - Update freesurfer tsv to match bids spec
- Update file name of Freesurfer dseg tsv
    @kaitj
    kaitj committed Dec 1, 2022
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  6. Copy zona tsv to appropriate directory 

    - Add inputs to rule all for copying freesurfer and zona tsv files to
appropriate location
    @kaitj
    kaitj committed Dec 1, 2022
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  7. update with smk version of python script

    @kaitj
    kaitj committed Dec 1, 2022
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  8. wip - changes for labelmerge rule 

    - Still need to fix piping of workflow, update entities, and filenames
    @kaitj
    kaitj committed Dec 1, 2022
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  9. fix conflicts, update dseg

    @kaitj
    kaitj committed Dec 1, 2022
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  10. add labelmerge placeholder 

    - Adds in rule for labelmerge (needs updating with container and proper
command)
- Update resources with correct names and paths
- Add tsv to rule all for copying from resource to bids folders for
labelmerge
- Simplify rule all
    @kaitj
    kaitj committed Dec 1, 2022
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  11. Update comment regarding transformation

    @kaitj
    kaitj committed Dec 1, 2022
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  12. fix FreesurferThal_dseg.tsv

    @kaitj
    kaitj committed Dec 1, 2022
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  13. add labelmerge container

    @kaitj
    kaitj committed Dec 1, 2022
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  14. snakefmt quality fixes

    @kaitj
    kaitj committed Dec 1, 2022
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  15. fix column headers for tsvs

    @kaitj
    kaitj committed Dec 1, 2022
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  16. add snakemake cores flag for labelmerge

    @kaitj
    kaitj committed Dec 1, 2022
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