A couple other things to check:
(1) That the voxel sizes are on the same scale between scans;
(2) Use a smaller smoothing kernel as well.
(3) Set the voxel size to the actual size, rather than multiplying by 10 or 20.
(4) Make sure the origin is the same in both images.
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 Mon, Feb 14, 2011 at 11:35 AM, Hekmatyar <[log in to unmask]> wrote:
> Thanks Dr. John
> I will check that, The orientation of anatomical before coregistration is
> same as orientation in the functional. I have attached some snapshots of
> display and checkreg.
> Those are from rat brains, I will try changing separation values as well.
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
> Behalf Of John Ashburner
> Sent: Monday, February 14, 2011 10:19 AM
> To: [log in to unmask]
> Subject: Re: [SPM] Orientation swap
> I'm not sure that any orientation has been swapped. The images are
> simply displayed in a way that uses the orientation images in the
> headers. If you show one of the images with eg the Display button,
> then the orientation in which the image is displayed will be
> determined by the orientation encoded in your image headers.
> As these do not appear to be human brains, I would perhaps suggest
> changing the values in the "Separation" option. When estimating the
> parameters, the algorithm only looks at the image every few mm (to
> save time). In the case of these images, every few mm is likely to
> mean that most of the information is unused. I notice that the joint
> histograms are very noisy. This should be fixed by using more of the
> Best regards,
> On 14 February 2011 15:08, Hekmatyar <[log in to unmask]> wrote:
>> Hello All
>> Could you please suggest me why the orientation of the images were swapped
> after co-registraton (snapshot of coregistration)? Thanks