read.ANALYZE function

I/O Functions

Read fMRI data from ANALYZE file(s).

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.

Returns

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

Author(s)

Karsten Tabelow tabelow@wias-berlin.de

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 .

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.

See Also

write.ANALYZE, read.AFNI

Examples

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