Add group directives to mrtpipelines.smk #12
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kaitj
commented
Oct 31, 2022
kaitj
commented
- Splits the processing into 3 phases
- Could consider splitting into 4 phases (an extra phase that separates tractography processing)
- Refactor notes and TODOs
- Remove "optional" GM exclusion for v0.1.0
- Fix bash "if" conditional for dwi2fod
- Conditions were for parameters were flipped (i.e. if empty vs non-empty)
- Add mention of ideal "step size" for tractography
- Splits the processing into 3 phases - Could consider splitting into 4 phases (an extra phase that separates tractography processing) - Refactor notes and TODOs - Remove "optional" GM exclusion for v0.1.0 - Fix bash "if" conditional for dwi2fod - Conditions were for parameters were flipped (i.e. if empty vs non-empty) - Add mention of ideal "step size" for tractography
kaitj
added
the
maintenance
tkkuehn
requested changes
Nov 2, 2022
dbsc/config/snakebids.yml
Outdated
| - group | ||
| - participant2 | ||
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| # Mapping from analysis_level to set of target rules or files | ||
| targets_by_analysis_level: |
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Need to update this to reflect participant1 and participant2 analysis levels.
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Fixed this in c258563 - this is actually still suppose to be participant and group. Got this part mixed up with the group directive usage within the .smk file.
| @@ -93,8 +94,8 @@ parse_args: | |||
| nargs: "+" | |||
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| --step: | |||
| help: '(Mrtrix3) set the step size of the algorithm in mm | |||
| (default: 0.35mm)' | |||
| help: '(Mrtrix3) set the step size of the algorithm in mm. Should set to | |||
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If we're going to include this recommendation it would be good to briefly explain why or give a reference.
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Added reasoning in 36529fd
Fixed participant levels to only have 'participant' and 'group'. Also fixed the group directive within snakemake, which is separate from the analysis levels.
tkkuehn
approved these changes
Nov 2, 2022
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