Hi - your command looks correct - what happens if you apply this
backwards transform to the standard space image instead of the ROI -
does that work?
Cheers.
On 16 Sep 2009, at 23:49, Vinod Venkatraman wrote:
> Hi,
>
> I am trying to register an ROI created in standard space to
> individual subject space and find that they are considerably
> displaced. As an illustration, I have defined a random ROI around
> then ventricles on the standard image. I then used the following
> command to transform it to subject space (based on the parameters
> from earlier first level registration).
>
> Flirt –in roi_standard.nii.gz –ref example_func.nii.gz –applyxfm –
> init standard2example_func.mat –out roi_subject.nii.gz.
>
> I have attached the original ROI overlay on standard image and the
> transformed overlay on the subject’s example_func image. As you can
> see, the transformed ROI is considerably displaced. Any ideas what I
> may be doing wrong here? The original registrations at the first
> level look fine.
>
> Thanks
> Vinod
>
> PS: I have also applied flirt as a two stage process going from
> standard to highres and then from highres to functional and results
> look the same.
>
> <roi_subject.png><roi_standard.png>
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