Hi Sandy,
If you'd like to use Matlab, there are some SPM5 functions that are pretty straightforward.

spm_vol and spm_read_vols (to read in a volume)
spm_write_vol (to write)

Typically, you can read in an existing nifti header with V = spm_vol(filename), read the image data with Y = spm_read_vols(V), then change the Y values to a make a mask, etc., change the filename in V.fname, and then write the new volume with spm_write_vol(V,Y). This is from memory, so check the help info on these functions.

hth,
Andy

---- Original message ----
>Date: Sun, 18 Feb 2007 14:08:02 -0800
>From: "[log in to unmask]" <[log in to unmask]>
>Subject: [FSL] writing values to a nifti file
>To: [log in to unmask]
>
> Hi FSLers,
>
> I was wondering if anybody could point me into the
> rigth direction with my question. I want to write
> specific values directly to xyz coordinates in a
> nifti file. Are there UNIX or Matlab based
> programs/scripts you can recommend that will do that
> in a somewhat straighforward manner?
>
> Thanks a lot,
>
> Sandy
>
>
>
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