> Thank you for that solution! By reorienting them to you mean adjusting
> pitch/roll/yaw and then clicking reorient images or is there another way I
> have to implement this?
This is the easiest way. The other way would be to write some code - although
a few people like to use tha Coreg button (with the template images) to
provide starting estimates.
Best regards,
-John
> On Thu, Sep 11, 2008 at 7:01 AM, John Ashburner
<[log in to unmask]>wrote:
> > My best guess is the usual one (which may have been repeated a few times
> > on the mailing list). Try reorienting your images before you use them in
> > SPM. If the origin is more than about 3cm from the AC, or the orientation
> > is out by more than about 15 degrees, then the initial affine
> > registration is likely
> > to mess up.
> >
> > Best regards,
> > -John
> >
> > On Sunday 07 September 2008 17:25, Cyrus Raji wrote:
> > > Hi, All
> > >
> > > So I've been attempting to run VBM 5 on a structural MRI image and I
> > > keep getting bad results for this one subject in particular (see
> > > picture). However, I do not believe that it is a problem with the scan
> > > itself
> >
> > because
> >
> > > when I run the unified segmentation using vbm, I get good results and
> >
> > when
> >
> > > I've segmented this scan with spm2/vbm2 in the past I've also gotten
> > > good results. My questions (for Dr. Gaser or any other VBM gurus are):
> > >
> > > 1. Why am I getting these discordant results between the vbm5 and spm5
> > > processing streams and how I do I fix the discrepancy?
> > >
> > > 2. If I want to do VBM, do I need to use the "estimate and write"
> > > options from the vbm5 toolbox? Why not just use the standard spm5
> > > processing stream?
> > >
> > > Any and all input is much much appreciated!
> > >
> > > Thank you,
> > >
> > > Cyrus
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