My best guess is that the image that you're trying to normalise hasn't
been well coregistered with the anatomical data. If the anatomicals
align well, then functional images that you warp the same way should
also be well aligned. Another possibility is that you have an older
version of SPM8 - without the more recent fixes.
Best regards,
-John
On Wed, 2010-02-10 at 10:49 -0800, Desmond Oathes wrote:
> Hi again,
>
> With some more checking, it seems that my group template is decently
> aligned with MNI (see 1st attached figure) but when I do the DARTEL
> normalization step, the brain is shifted back in the y-axis. It
> doesn't look stretched, to me, so much as shifted. Have others had
> this trouble with the DARTEL normalization? Any suggestions on how to
> fix it?
>
> Thanks!
> Desmond Oathes, Ph.D.
> Stanford Psychiatry
>
>
>
> On Tue, Feb 9, 2010 at 9:10 PM, MCLAREN, Donald
> <[log in to unmask]> wrote:
> (1) I'd recommend against using the spmT maps for the input to
> the second level, the spmT maps are a measure of the fit of
> your model and not the amplitude of the response. Instead, you
> should use the con* images as the inputs and compare the
> amplitudes across subjects.
>
>
> (2) I suspect that the homogeneous border is the result of the
> DARTEL smoothing process. I would look at each individuals
> transform to see if you get a stretching effect that has been
> noted by others in each subject. This would give you a more
> direct indication of the problem compared to looking at the
> second level results.
>
>
> (3) How well do the individual subject maps line up with MNI
> space after the transformation? It looks like your getting
> significant results in the skull -- which I would've thought
> would be in the homogeneous section of the brains.
>
> Best Regards, Donald McLaren
> =================
> D.G. McLaren
> University of Wisconsin - Madison
> Neuroscience Training Program
> Office: (608) 520-0586
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> On Tue, Feb 9, 2010 at 10:59 PM, Desmond Oathes
> <[log in to unmask]> wrote:
> Hi Guys,
>
> Something funny seems to be happening with my DARTEL
> normalization step. The DARTEL template looks good
> and even lines up well with MNI. For normalization, I
> use my newly formed DARTEL template (least smooth
> version), plug in the flow fields for each subject,
> and try to normalize my spmT images. The resulting
> images that I look at with 2nd level results seem to
> have been padded with gray homogenous borders around
> the brain leading to spurious activations outside of
> the brain (see attachment). What did I do wrong? I
> can send out the job file for the normalization, if
> that's helpful, too.
>
> Grateful for any help,
>
> Desmond J. Oathes, Ph.D.
> Stanford Psychiatry
>
>
>
--
John Ashburner <[log in to unmask]>
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