I used the latest spm8 release and repeated the same steps. Unfortunately I got the same problem (see the figure attached). In the figure I labeled the template, flow field, and a functional scan before and after normalizing.
Mostly I used default values, for voxel sizes I used [3 3 3]. In segmentation, I used medium regularization.
This time I used the latest SPM8 patches.
> Date: Tue, 24 Jul 2012 16:25:52 +0100
> From:
[log in to unmask]> Subject: Re: [SPM] DARTEL - Normalize to MNI space problem
> To:
[log in to unmask]>
> I assume that the registration was run using the GM and WM segmented
> from anatomical scans. If you want to apply transformations estimated
> from anatomical scans to fMRI data of the same subjects, then (for
> each subject) the fMRI data should be coregistered so that they align
> with the anatomical scan. You can assess this using Check reg.
>
> Also, ensure that you use the latest patches for SPM8. The original
> version of normalise to MNI space had a few problems - although these
> were soon fixed.
>
> Best regards,
> -John
>
>
> On 24 July 2012 16:12, soha saleh <
[log in to unmask]> wrote:
> > Hello:
> >
> > Recently I started using DARTEL for preprocessing scans of subjects with
> > lesions due to stroke. So I do not have much experience in it.
> > I used the segment tool and a map of the lesion created in mricro as a
> > mask.
> >
> > The templates were created with no problem but I have a problem with
> > normalizing functional scans to the template.
> > The sw.* images are getting warped abnormally. The figures might give you
> > an idea what I mean.
> >
> > I tried to coregister and align the functional scans to the template before
> > normalizing them but that did not help (see the figure in the second file).
> >
> > I appreciate if anybody has a suggestion or a solution to such problem.
> >
> > Thank you!
> >
> > Regards,
> >
> > Soha
> >
