John,
I was just looking into this and found the same thing. Different rp file
values with reoriented images.
hdr(1).private.mat
-3.0000 -0.0000 0 97.5000
-0.0000 3.0000 0.0000 -96.9129
0.0000 0 4.5000 -56.4129
0 0 0 1.0000
hdr(1).private.mat0
-3.0000 0 0 97.5000
0 3.0000 0 -96.9129
0 0 4.5000 -56.4129
0 0 0 1.0000
and reoriented file:
hdr2(1).private.mat
-3.0000 -0.0000 0.0000 97.5000
0.0000 3.0000 0.0000 -56.9129
-0.0000 0 4.5000 -86.4129
0 0 0 1.0000
hdr2(1).private.mat0
-3.0000 0 0 97.5000
0 3.0000 0 -96.9129
0 0 4.5000 -56.4129
0 0 0 1.0000
It looks like the .mat fields are slightly different; however, the same for
all volumes. The question is thus, why are the realignment parameters
different if the same data is used, just different transformation matrices.
Additionally, since the rp files are different, using the motion regressors
as covariates would change the models as well.
Are the differences due to interpolation to produce the mean image
resulting in slightly different values?
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Office: (773) 406-2464
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On Fri, Nov 25, 2011 at 3:43 PM, John Ashburner <[log in to unmask]>wrote:
> I don't have any ideas here. I think you really need to take a close
> look at the data. You can read the fields in the headers by:
>
> P='blah.nii';
> Nii=nifti(P)
>
> If you want to see the actual values, then you can look at a hidden
> field of the nifti object:
>
> Nii.hdr
>
> Computing difference images via ImCalc, and displaying them via
> CheckReg can also help to give clues.
>
> Best regards,
> -John
>
> On 24 November 2011 10:53, Joshua Balsters <[log in to unmask]> wrote:
> > Dear SPMers
> >
> > I found one previous discussion on this point but not much else, so
> apologies if I'm repeating what everyone already knows.
> >
> > I've recently starting using 4D files straight from the scanner (Philips
> Acheiva) in SPM rather than splitting them into 3D files using fslsplit.
> I'm finding in most cases there are subtle (+/-0.5mm) to drastic (over 2mm)
> differences in my realignment parameters depending on whether I use the 4D
> or 3D versions of the same datasets. These differences are only in the
> translations and not the rotations.
> >
> > It would be great if anyone could explain why this happens. I had a
> quick look for differences between the 3D and 4D files and I think the
> issue is that fslplit is automatically changing my datatype from int16 to
> float32, and i read in a previous discussion that it also changes the
> scaling factor which is probably the bigger issue.
> >
> > any advice on this issue would be greatly appreciated!
> >
> > Best
> > Josh
> >
>
