FEAT: Generate BOLD reference using low FD frames calculated by MCFLIRT#553
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joey-scanga wants to merge 15 commits into
Open
FEAT: Generate BOLD reference using low FD frames calculated by MCFLIRT#553joey-scanga wants to merge 15 commits into
joey-scanga wants to merge 15 commits into
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run mcflirt on raw BOLD data, then use the lowest absolute motion frame as the boldref
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #553 +/- ##
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- Coverage 61.64% 61.61% -0.03%
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Files 73 73
Lines 7057 7075 +18
Branches 868 871 +3
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+ Hits 4350 4359 +9
- Misses 2438 2447 +9
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Add a new keyword for
--hmc-bold-frame, "mcflirt", which creates a BOLD reference frame for within-run alignment by running MCFLIRT on the raw BOLD data (using the "normcorr" function) to calculate FD, then RobustAverage'ing together the 5 lowest-FD frames (using the 'FSL' mc_method).In my lab's data this seems to create better reference frames than the 'auto' heuristic method