This is because the headers are written in NIfTI-1 format, which is a format
supported by FSL, AFNI, BrainVoyager, SPM and many other tools. See
http://nifti.nimh.nih.gov/ for more information. I think Chris has
re-written MRIcro to support NIfTI-1 (according to
http://www.sph.sc.edu/comd/rorden/mricro.html ). Maybe you have an older
version.

Best regards,
-John

On Friday 03 February 2006 10:03, Dresner, Alex wrote:
> Dear John, SPM List,
> This is possibly unrelated to the unwarping error, but we're seeing some
> odd behaviour in 3-D Analyze headers using SPM5 (with update 411
> installed). I've attached headers before and after slice timing
> correction--according to MRIcro the origin is moving from (64,64,22) to
> (512,999,0), which as you might imagine is causing some difficulties in
> overlays. The data is 128x128x44. Much of the other header information has
> become garbled as well (non-English characters in various fields). I've
> just attached the headers, but can send the images (unremarkable EPI).
> SPM's Display function still thinks the origin is at (64,64,22). We're
> using Matlab 7.01 or 7.1 (R14 SP3) on Windows XP machines. This seems to
> be our header output for anything coming out of SPM5--the betas, con files
> and spmT maps shows an origin of (512, 0, 0). Any ideas what could be
> causing this?
> Thanks for your assistance,
>
> Alex
>
> **********************
> Alex Dresner, Ph.D.
> fMRI Physicist
> Imaging Sciences Department
> Hammersmith Hospital
> Imperial College London
> 020 8383 4516 (w)
> **********************
>
> From: SPM (Statistical Parametric Mapping) on behalf of John Ashburner
> Sent: Wed 01/02/2006 18:39
> To: [log in to unmask]
> Subject: Re: [SPM] a question
> Hi Alexa,
>
> > Do you mean by this that reslicing at realignment (or just for realign &
> > unwarp?) are faulty prior to the recent updates and including spm5b?
>
> Its only the reslicing and unwarping - as far as I know. The fix is
> mentioned in
> ftp://ftp.fil.ion.ucl.ac.uk/spm/spm5_updates/Updates_README.txt
> ------------------------------------------------------------------------
> r403 | john | 2006-01-13 18:17:18 +0000 (Fri, 13 Jan 2006) | 2 lines
> Changed paths:
> M /trunk/spm_uw_apply.m
>
> Fixed a very nasty bug in spm_uw_apply.m.
>
> ------------------------------------------------------------------------
>
> > Or is
> > this just a matter of display? I'm perhaps being slow on the uptake here
> > but don't quite understand the description of the problem - would you
> > mind clarifying? Thank you!
>
> Normally, when images are realigned, their orientations are changed. This
> is done in the .hdr files of NIFTI images (it used to be done via the .mat
> files in previous versions). When these images get resliced, the
> orientation information of the first image is put in all the headers of the
> resliced images. The idea here is that the first image remains stationary,
> and should be in the same orientation as the resliced images.
>
> My bug in spm_uw_apply.m was that the image orientations of the unwarped
> and resliced images were copied from the realigned images - rather than
> being the orientation of the first image.
>
> > And while I'm at it, thanks for for the new 'parallel' style GUI &
> > documentation :)
>
> You're welcome.
>
> All the best,
> -John
>
> > On Feb 1 2006, John Ashburner wrote:
> > >> I have a problem in using SPM5 and i was wondering if you could help
> > >> me with it. I was just trying to align some fMRI datasets using SPM5.
> > >> The thing is that once I "Realign and Unwarp" the data set and saved
> > >> the resliced images. Afterwards I once again estimated the realigned
> > >> the unwarped dataset to see how good it is realigned. Surprisingly the
> > >> surves that I recieved is almost the same as the raw data ! It means
> > >> that almost nothing has happened in previous step (Realign and
> > >> Unwarp)!
> > >
> > > A bug was introduced into the code, which I think was my fault. This
> > > one was fixed by the last batch of updates for SPM5.
> > >
> > >What was happening was that the wrong orientation information was being
> > >written into the headers of the resliced and unwarped images.
> > >
> > >Best regards,
> > >-John