MRI Preprocessing

Tools

• preprocessMprage
• preprocessFunctional
  • sliceMotion4d
• ROI_TempCorr.R

Output scheme

preprocessFunctional prepends each processing step as a prefix to each input, creating files like brnaswutm_func.nii.gz. In reverse order (order of name), the posible steps are:

prefix	desc
A	Auto Correlation removal (optional)
b	Bandpass filtering (optional, simultaneous with regression, for rest)
g	Global signal regression (optional, label optional, part of r)
r	Nuisance regression (optional)
n	Intensity normalization
f	High-pass filtering (optional, simultaneous with regression, for task)
a	ICA-AROMA (optional, requires warp)
s	Smoothing
w	Co-registration and warping to standard space (spatial normalization, optional)
u	Field map unwarping (optional; Susceptibility Distortion Correction)
d	Intensity/wavelet despiking (optional)
k	Skull stripping and intensity thresholding
mt	4D slice-time motion correction (sliceMotion4d)
m	Motion correction
t	Slice timing correction
p	Physio/retroicor (optional)
0	truncate (optional, if scanner output includes disacq)
_	fslorient

Depends

see bibtex or plain text 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.