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ins-amu / tvb-pipeline

INS TNG pipeline for TVB simulations
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Enable DWI preprocessing #1

Open maedoc opened 2 years ago

maedoc commented 2 years ago

DWI preprocessing has been a TODO in this repo for a while. Mrtrix3's combination of denoising and FSL preprocessing should still be used even when lacking RPE.

maedoc commented 2 years ago 
$ dwidenoise raw.mif raw_denoise.mif
$ mrconvert -set_property TotalReadoutTime 0.01 raw_denoise.mif raw_denoise_trt.mif
$ dwifslpreproc -rpe_none -pe_dir j- raw_denoise_trt.mif rawpp.mif -eddy_options="--slm=linear"

where j- is from 

$ mrinfo raw.mif | grep Enc
  PhaseEncodingDirection: j-

(not sure why it doesn't figure that out itself) and the -eddy_options="--slm=linear" is a recommendation of the dwifslpreproc script itself for this dataset which has an asymmetric gradient scheme. The total readout time bit is arbitrary but ok, cf here