Write data to a file in ANALYZE 7.5 format.

Write an array or vector to the two files that make up an ANALYZE 7.5 image: a 348 byte header (<base>.hdr) and the raw voxel data in a separate file (<base>.img).

Usage

write.analyze(filepath, analyzedata, analyzeheader = NULL, ...)

Arguments

filepath

character string, the path of the output files. It must end with .hdr or .img (optionally followed by .gz), or contain no extension at all, in which case the two file names are derived from it by appending .hdr and .img. See analyze.pair.files.

analyzedata

array of numeric (integer or double) data, can have up to 7 dimensions. See analyzeheader.for.data for how the data type is chosen, and note that the data type and the number of bits per value in the header have to match the data, otherwise the file is not readable.

analyzeheader

optional ANALYZE 7.5 header that is suitable for the passed analyzedata, see analyzeheader.for.data and analyzeheader.template. If not given, one is generated from the data, with all other fields set to the defaults of the format, i.e. the voxel sizes in pix_dim will be zero and you most likely want to set them.

...

additional parameters passed to analyzeheader.for.data. Only used if analyzeheader is NULL.

Value

invisible named list with the entries header (the header that was written) and data (the data that was written). Use these to check what the function did with your input, they reflect the values that ended up in the file, e.g. values that had to be converted to the data type stated in the header.

Note

ANALYZE 7.5 cannot store a transformation matrix, and the format does not even define the direction of the voxel axes in world space. This writer therefore cannot write the geometry of an image: if you have a volume with a known vox2ras_matrix and you want to keep it, write a NIFTI v1 file with write.nifti1 instead (either a single file, or a .hdr/.img pair by setting the header magic to 'ni1', which is what write.fs.volume does for such file names). If you know that the data will be read by SPM or FreeSurfer, you can store the image origin in the spm_origin field of the header, see read.analyze.header.

Note that tools differ in how they recognize the format. FreeSurfer's mri_convert, for example, does not infer the ANALYZE format from the .hdr file extension and reports 'cannot determine file type' unless the input type is given explicitly: mri_convert -it analyze -ot mgz vol.hdr vol.mgz works, mri_convert -ot mgz vol.hdr vol.mgz does not. The header written by this function is the one FreeSurfer itself writes for -ot analyze, so this is a limitation of the reader, not of the file.

See also

read.analyze.header, analyzeheader.for.data

Examples

outfiles <- tempfile()
data <- array(1:24, dim = c(4, 3, 2))
analyzeheader <- analyzeheader.for.data(data)
analyzeheader$pix_dim <- c(1., 1.5, 1.5, 2., 0., 0., 0., 0.)
write.analyze(outfiles, data, analyzeheader)
vol <- read.fs.volume.analyze(outfiles, with_header = TRUE)
vol$header$pix_dim
#> [1] 1.0 1.5 1.5 2.0 0.0 0.0 0.0 0.0