Dear Donald,
That was my immediate thought as well. However, I've coregistered the
T1 image to the mean functional image (output from the Realign:Unwarp
module) for every subject. I have verified that the alignment between
the T1 and functional images is within acceptable parameters for the
standard Segment+ normalise procedure for all subjects, having already
performed 1st and 2nd level analyses that I am hoping to compare with
the DARTEL normalised data.
Comparing the original T1, the Template, the flow field and the mean
functional image yields the following for the two subjects (out of 39) I
have used to test DARTEL as of yet.
It seems like the normalisation procedure flips the EPI's for some, to
me, obscure reason.
Would skull stripping the images help in any way?
Best wishes,
h.
On 28.09.2009 16:31, MCLAREN, Donald wrote:
> Looks like your EPI images are aligned to the T1 images in native space
> (orientation is different). Use check reg to see if the native space EPI
> is aligned to the native space. If not, then you will need to align them
> first and make sure the orientations are the same.
>
> On Mon, Sep 28, 2009 at 4:49 AM, Haakon Engen
> <[log in to unmask] <mailto:[log in to unmask]>>
> wrote:
>
> Dear SPM'ers,
>
> I'm running into some weirdness using DARTEL to normalise my
> functional images. I have followed the recommended processing
> pipeline in the manual, using the "New Segment" module to create
> preimported rc*.img files that I've fed into the "Create templates"
> module.
>
> After normalising the data the results don't look too good, as you
> can see from the attached images. The functional images are severely
> distorted, while the flow fields and template looks fine (albeit
> from my limited understand of what fine DARTEL output is). Can
> anyone help me figure out where I've messed up?
>
> Please let me know if you need any more information.
>
> Best wishes,
> h.
>
>
>
>
> --
> Best Regards, Donald McLaren
> =====================
> Support the Alzheimer's Association Memory Walk 2009 ~~~
> Join the Wisconsin Alzheimer's Disease Research Center team or make a
> donation.
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>
>
> =================
> D.G. McLaren
> University of Wisconsin - Madison
> Neuroscience Training Program
> Office: (608) 265-9672
> Lab: (608) 256-1901 ext 12914
> =====================
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