Dear Roman,
I just started to use the Nifti complient follow up program of MRIcro,
named MRIcron, also made by Chris Rorden. See:
http://www.sph.sc.edu/comd/rorden/mricron/
I just finished my first spm5 analyses, and reoriented, not resliced,
images seem to display well (e.g, the orientation in the nii header
bytes is taken into account!) with respect to anatomical images with
different orientations and voxel sizes. But beware that I only did a few
tests to see, you'd better also test it with your data.
From the website of MRIcro and MRIcron I get the impression that MRIcro
will not be made fully Nifti-complient (it reads nifti now, but displays
only the raw content, eg no angulation included), and that one should
move to mricron which does. And that is agreeing with my first
experiences with both programs.
Chris, correct me if I'm wrong!
So no need anymore to reslice in order to display overlays outside of
SPM when you use a nifti 1.0 complient viewer!
The mat-file nightmare is finally over...
Good luck,
Bas
Roman Rodionov wrote:
> Dear List,
>
> I've learnt that SPM5 saves info about reorientations of an image to .hdr
> file. As image file saved by SPM5 is a NIFTI file the header is embedded
> into .img file. So MRIcro can't visualise reoriented image unless changes
> made in the .hdr file are not copied into .img file.
>
> I think I'm not the first who encountered with this issue. Could you please
> let me know if there is a script (in SPM5 of the separate one) which copies
> header info from .hdr file into proper place in the .img file?
>
> Best wishes,
> Roman
>
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
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