Did you coregister the T1 to the functional images *after* running
DARTEL? If so, the "native" space is different for the flow fields and
the functionals, which might explain the oddities that you are seeing.
-Neil
Haakon Engen wrote:
> 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.
>> http://madison.kintera.org/2009/donaldmclaren
>>
>>
>> =================
>> D.G. McLaren
>> University of Wisconsin - Madison
>> Neuroscience Training Program
>> Office: (608) 265-9672
>> Lab: (608) 256-1901 ext 12914
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