gradnonlincorr: Perform Gradient Nonlinearity Correction

In mathesong/kipettools: R Tools For KI PET Group Files

Perform Gradient Nonlinearity Correction

Description

This function wraps around FreeSurfer, with MATLAB installed, and the dev MATLAB files in the correct folders. I've written a guide to installing this which I'll hopefully put online soon, but contact me if you need this function and don't have it. This function modifies the file in place, and saves everything else either in the same folder, or elsewhere.

Usage

gradnonlincorr(
  nii_filename,
  inpath = getwd(),
  coeff_file,
  outpath_checks = NULL,
  checkLines = F,
  bids_sidecar_heurcheck = T,
  bids_sidecar_exists = T,
  unwarp_sh_path = ""
)

Arguments

nii_filename	Filename of the input nii file. With or without file extension
inpath	Path to the input file. Defaults to working directory.
coeff_file	Filename of the coefficient file. It should be placed in a special folder and named a particular way, but this information is or will be in the setup guide.
outpath_checks	Path for the extra images for checking to be placed into. If not specified, they will be kept in the same folder.
checkLines	Should the system commands be checked (and not run)? Default FALSE.
bids_sidecar_heurcheck	If it is not explicitly stated in the sidecar whether correction has been applied, this checks the sidecar for heuristic signs. This is, however, not guaranteed to come to the correct answer, depending on the MR system. Default is TRUE.
bids_sidecar_exists	Defaults to TRUE. Set this to FALSE in case of there not being a BIDS sidecar.
unwarp_sh_path	Optional file path to the location of the unwarping .sh file. If it is chmodded and added to the system path, this should not be necessary, but otherwise, one can specify its location.

Value

This function modifies the file in place, saves all the other files to check, and returns the outcome from the terminal.

Examples

gradnonlincorr("sub-01_T1w", coeff_file='coeff_avanto.grad')

mathesong/kipettools documentation built on Feb. 5, 2024, 10:10 p.m.