Add slice-time correction to preprocessing

mwaskom / lyman

Data pipelines and analysis library for functional MRI

http://www.cns.nyu.edu/~mwaskom/software/lyman

BSD 3-Clause "New" or "Revised" License

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Add slice-time correction to preprocessing #107

Open mwaskom opened 7 years ago

mwaskom commented 7 years ago

This should be added while remaining optional. A few thoughts:

Probably easier to do in Python with spline interpolation than calling out to FSL.
Need to determine the best way to specify slice times
Should it be it's own node or should it be wrapped into the FinalizeTimeSeries interface to minimize loading/saving of the time series?

mwaskom commented 7 years ago

See http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182939

What probably make sense is to do slice time correction in the first step of the preprocesing workflow, then write out the individual volumes of the slice-time corrected data (for later resampling) and the full time series of the uncorrected data (used to estimate motion but not later resampled).