read.ANALYZE: I/O Functions

In fmri: Analysis of fMRI Experiments

I/O Functions

Description

Read fMRI data from ANALYZE file(s).

Usage

read.ANALYZE(prefix = "", numbered = FALSE, postfix = "",
             picstart = 1, numbpic = 1, level = 0.75, mask=NULL, setmask=TRUE)

Arguments

prefix	string(s). part of the file name before the number or vector of strings for filename (if numbered is FALSE)
numbered	logical. if FALSE only prefix is taken as file name (default).
postfix	string. part of the file name after the number
picstart	number of the first image to be read.
numbpic	number of images to be read
level	Quantile level defining the mask
mask	array or nifti-object containing the mask. If set this replaces the mask defined by argument level.
setmask	Logical (default TRUE), whether to define a suitable mask based on level

Details

This function reads fMRI data files in ANALYZE format. If numbered is FALSE, only the vector of strings in prefix is used for file name (default).

If numbered is TRUE, it takes the first string in prefix and postfix and a number of the form "007" in between to create the file name.

The number is assumed to be 3 digits (including leading zeros). First number is given in picstart, while numbpic defines the total number of images to be read. Data in multiple files will be combined into a four dimensional datacube.

Value

Object of class "fmridata" with the following list entries:

ttt	raw vector (numeric size 4) containing the four dimensional data cube (the first three dimensions are voxel dimensions, the fourth dimension denotes the time).
header	header information of the data
format	data source. string "ANALYZE"
delta	voxel size in mm
origin	position of the datacube origin
orient	data orientation code
dim	dimension of the datacube
weights	weights vector coding the relative voxel sizes in x, y, z-direction
mask	head mask

Note

Since numbering and naming of ANALYZE files widely vary, this function may not meet your personal needs. See Details section above for a description.

Author(s)

Karsten Tabelow [e-mail]

References

Biomedical Imaging Resource (2001). Analyze Program. Mayo Foundation.

Polzehl, J. and Tabelow, K. (2007) fmri: A Package for Analyzing fmri Data, R News, 7:13-17 .

See Also

write.ANALYZE, read.AFNI

Examples

 ## Not run: analyze <- read.ANALYZE("analyze",TRUE,"file",31,107)

fmri documentation built on Sept. 11, 2024, 7:58 p.m.