Hi Joseph,
Have tried the 'example of creating a simulated .NII file'
by Tom Nichols and John Ashburner at

Maybe you can try duplicating the slices in case SPM
do not like only one image slice...


Date: Fri, 15 May 2009 14:33:10 +0100
From: [log in to unmask]
Subject: [SPM] converting to nifti
To: [log in to unmask]


Does anyone know how to convert matlab files into .nii files
that can be read by SPM. I am trying to use SPM to analyse
some optical imaging data.

I have arranged my data into a 4D struct [x y z t] although 
it is not fMRI data there are only 2 spatial dimensions so
I have 60 frames of 512x512 14 bit images arranged in a
matlab file as (512,512,1,60).

I used the make_nii function that is available in the MatLab
NIFTI and ANALZYE toolbox, and although it seems to work
and it creats an image file with a header etc, when I save
it as a .nii file I am still unable to open it with SPM.

Maybe I'm barking up the wrong tree in thinking I can treat
my optical imaging data like fMRI data, but my supervisor is
convinced I can use SPM with optical imaging data.

Any advice ot information would be much appreciated



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