For 4D files, there is a seperate .mat file generated to save the extra affine
transform matrices. SPM makes use of this, but other software doesn't.
Best regards,
-John
On Friday 26 December 2008 19:09, Neil Chatterjee wrote:
> So here's what's happening. For nifti, all 185 volumes for each run are
> stored as one 4D image. The SPM file selector, by default, only selects
> the first volume in a 4D image. So while you are trying to input 5 sets of
> 185 volumes, you are in fact only inputting 5 volumes.
>
> There's an easy enough way to select all 185 volumes. To do it, change the
> '1' under the filter box to '1:185' and then select all the resulting
> volumes.
>
> That said, this still WILL NOT give you proper realignment results! In 4D
> nifti files, all of the volumes share one common header. Because
> realignment works by changing the volume headers *relative* to each other,
> realignment will NOT work if the volumes do not have separate headers! For
> 4D files, realignment will look like it's executing perfectly, but at the
> end all the volumes in any 4D file will be in the same orientation as the
> last volume in the file. Perhaps reslicing fixes the problem (perhaps it
> doesn't), but I never reslice during realignment anyways. Ultimately, in
> order to perform a proper realignment, each 4D file must be decomposed into
> separate single volume (3D) nifti files (185 of them in your case). I use
> fslsplit to do this, but perhaps there is some way native to SPM to do it
> as well. Once all the files are in 3D nifiti format, you can carry out
> realignment just as you did using analyze format.
>
> Hope this helps,
> -Neil
>
> Neil Chatterjee
> Research Assistant
> Stanford University Systems Neuroscience and Pain Lab
> [log in to unmask]
> (650)-724-0522
>
> On Fri, 26 Dec 2008 08:22:05 -0500, Yune Lee <[log in to unmask]> wrote:
> > Dear SPMers,
> >
> > I'm thinking of converting from analyze format to nifti format and as a
> >first attempt, I compared the realignment results with nift format to that
> >with analyze format.
> > Turns out the realignment with nifti not only takes too quick (a couple
> > of seconds) but also looks quite different from that with analyze format.
> > The big difference is that there are only 5 nifti files (one for each
> > run) wheras there are 925 analyze files (185 per each run) for the 5 runs
> > of the same subject.
> > So, SPM5 seems to think that there is only 5 files reardless of the file
> >format. If the results look consisten, nonetheless, I would assume that
> > it's all good. But,
> > I'm not sure if the way I did was correct (I took the same step of
> >realignment that I used to do with analyze format. : select all files->
> >estimate & reslice-> leave others as default).
> > Attached are the results of two different formats. I wonder how people do
> >preprocessing using nifti format and any help would be much appreciated.
> >
> > Thanks,
> > YSL
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