niftiImage2fmri function

Create fmridata object from niftiImage

Transforms a niftiImage (created by readNifti from package RNiftyReg) into an object with class fmridata

niftiImage2fmri(niftiobj, level = 0.75, mask=NULL, setmask = TRUE, indx = NULL,
   indy = NULL, indz = NULL, avoidnegs = FALSE)

Arguments

• niftiobj: an object of class niftiImage
• level: quantile used in mask definition
• mask: array or nifti-object containing the mask. If set this replaces the mask defined by argument level.
• setmask: if TRUE create a brain mask
• indx: index vector for subcube definition
• indy: index vector for subcube definition
• indz: index vector for subcube definition
• avoidnegs: if TRUE change the mean to avoid negative image intensities

Details

This function can be used in connection with readNifti from package RNiftyReg to read large fMRI series from nifti files. The resulting fmridata-object stores the image data as 2 byte integer in raw format, in contrast for the 4 byte real used with other functions.

Returns

an object of class fmridata

Author(s)

Joerg Polzehl polzehl@wias-berlin.de

See Also

read.AFNI, read.DICOM, read.ANALYZE, read.NIFTI