Hi, John,
I don't think I changed orientation settings. Indeed in our lab the matrices in SPM.mat and t-test images are identical. The example I gave was from Emily.
I am using SPM2.
Xu
-----Original Message-----
From: John Ashburner [mailto:[log in to unmask]]
Sent: 2006年5月23日 4:23
To: Xu Cui; [log in to unmask]
Subject: Re: [SPM] left/right in SPM.mat and T-test image
Have you changed the image orientation settings at any point? Are you
exchanging data with someone who has different settings? Which SPM version
are you using?
Best regards,
-John
On Monday 22 May 2006 17:32, Xu Cui wrote:
> Hi, SPMers,
>
> I am wondering if anybody knows why the coordinate conversion matrices in
> SPM.mat and the resulted T-test image files are sometimes different. For
> example,
>
> By loading 'spmT_0003.img' alone (using spm_vol and spm_read_vols), the
> matrix is (e.g.) -3 0 0 81
> 0 3 0 -114
> 0 0 3 -54
> 0 0 0 1
>
> By loading spm.mat:
> SPM.xY.VY(1).mat =
> 3 0 0 -81
> 0 3 0 -114
> 0 0 3 -54
> 0 0 0 1
>
> We can see that the first row is flipped.
>
> This difference actually accounts for the left/right flip of xjview (xjview
> uses the matrix of the t-test image file while SPM uses that of SPM.mat).
> Emily and I have exchanged emails regarding this issue but we could not
> figure this out. Any feedback is appreciated.
>
> Many thanks,
> Xu
>
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
> Behalf Of Emily Stern Sent: 2006年5月22日 7:49
> To: [log in to unmask]
> Subject: Re: [SPM] Feeding my own T-map (in analyze format) into SPM
>
> Hi Ruth, Ged, and Chris,
> A word of caution when using xjview. There have been some recent issues
> where it became apparent that it may be flipping hemispheres. Otherwise,
> it's a great program.
> Emily
>
> >>> Christopher Summerfield <[log in to unmask]>
>
> 05/22/06 5:39 AM >>>
> hi Ruth & Ged,
>
> once you know the FDR-corrected t-value, then it's easy to threshold
> your
> image at that level using xjview
>
> http://people.hnl.bcm.tmc.edu/cuixu/xjView/
>
> all the best,
> Chris
>
>
>
> Christopher Summerfield
> [log in to unmask]
>
> On Mon, 22 May 2006, Ged Ridgway wrote:
> > Hi Ruth,
> >
> > I'm also interested in doing this. So far I've worked out that we
> > could use something like:
> >
> > t_crit = spm_uc_FDR(0.001,df,'T',1,tmap_vol)
> >
> > to find the t-threshold corresponding to FDR correction at the 0.001
> > level, where df is the number of degrees of freedom for the t-map, and
> > e.g. tmap_vol = spm_vol('your_tmap.img'). I think this is right for
> > both spm5 and spm2. (see e.g. help spm_uc)
> >
> > Thresholding the t-map is then simple, but I've not yet investigated
> > how to get the thresholded map into the results window. I think it may
> > be necessary to create a basic spm.mat with an appropriate
> > structure, but I'm not sure what the minimal set of fields would be.
> >
> > You'll probably get a more complete answer from someone like John; if
> > not, I'll try to have a look and get back to you if I work it out...
> >
> > Best,
> > Ged.
> >
> > Ruth Heller wrote:
> > > Hi,
> > > I've got my own T-map (in analyze format) that I would like to feed
>
> into SPM in
>
> > > order to correct for multiple comparisons and display the results
>
> using its
>
> > > graphics window. Is there a way to feed my map into SPM (instead of
>
> feeding the
>
> > > original data and performing the whole analysis in SPM)?
> > > Thanks,
> > > Ruth
> > >
> > >
> > >
> > > ----------------------------------------------------------------
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>
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