MRI Preprocessing

Tools

• preprocessMprage
• preprocessFunctional
  • sliceMotion4d
• ROI_TempCorr.R

Depends

see citations and preprocessFunctional -check_dependencies

• ROBEX
• ANTs
• FSL
• ICA-AROMA
  • v4 aroma: https://github.com/rtrhd/ICA-AROMA
  • orig repackages as ica_aroma: https://github.com/WillForan/ICA-AROMA/tree/maartenmennes-setup.py
• AFNI
• MNI2009c
• Brain Wavelet ToolboX
• NiPy(4dslicewarp)

Testing

Limited testing using bats in test/. see make test (Makefile)

See also

• fmriprep, clpipe, xcp-d
• afni_proc

Usage Notes

ROI Temp Corr

Running ROI_TempCorr.R is internally parallelized (default njobs=4). If you are also forking in e.g. a bash for loop like ROI_TempCorr.R ... & (and maybe paired with lncdtool's waitforjobs, some care will need to be taken to not hit a R parallel package socket port conflict.

1. the easiest solution is to disable internal parallelization: ROI_TempCorr.R ... -njobs 1.
2. Alternatively, you can manually set the port for each ROI_TempCorr.R. Consider

ROI_TempCorr.R ... -port "$((11290 + $(pgrep -caf ROI_TempCorr) ))"

FYI OSS

The code is "for your information." There are no plans (or avaiable resources) to support external usage.