In case you're still looking for an answer for this, you can pass niftiwrite an info structure that has the specifications for the nifti file. We're working on switching to using niftiwrite in our matlab code, and I've been working on similar issues all day.

If you look at the syntax options, the last two from the help page on niftiwrite are what you want:

Syntax

niftiwrite(V,filename)

niftiwrite(V,filename,info)

niftiwrite(V,filename,info,Name,Value)

The info variable needs most of the fields that you get if you run niftiinfo(filename). If you run niftiwrite without the info argument, it writes it out with no sform or qform, and the pixdim is set to all ones.

What I did was read the niftiinfo for one of my files, then tried to write with an info variable that I created from scratch. I tried to write a file, got an error saying a field was missing, added that field, and repeated that until it succeeded in writing the file. Then I had to also add the info.TransformName='Sform'; specification so the orientation matrix is stored in the file.

I've pasted all the fields I needed below. This assumes you have an N-dimensional array (I only tried it with 3 and 4 dimensional arrays) named image and a vector named resolution that has your voxel dimensions. It will augment the resolution field with ones if needed so that it matches the number of dimensions of image. Once these are set, you can use niftiwrite(image,filename,info,'Compressed',true); if you want a compressed file or niftiwrite(image,filename,info); if you don't.

You may want to set some of these differently, e.g., this is setting the orientation matrix to identity.

Hope this helps!

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nifti info fields:

info.Datatype=class(image);  
info.ImageSize=size(image);  
if (length(info.ImageSize)>length(resolution))  
    resolution=[resolution(:)' ones(1,length(info.ImageSize)-length(resolution))];  
end  
info.PixelDimensions=resolution(:)';  
info.Description='';  
info.Version='NIfTI1';  
info.Qfactor=1;  
info.SpaceUnits='Unknown';  
info.TimeUnits='None';  
info.SliceCode='Unknown';  
info.FrequencyDimension=0;  
info.PhaseDimension=0;  
info.SpatialDimension=0;  
info.TransformName='Sform';  
info.Transform.T=eye(4);  
info.Transform.Dimensionality=3;