Unfortunately no.
They were coregistered as per standard preprocessing protocol (i.e.
Realign:Unwarp>Coregister T1 to mean functional> New Segment> DARTEL
template creation on rc1 and rc2> Normalise to MNI space).
h.
On 28.09.2009 19:52, Neil Chatterjee wrote:
> 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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>>
>>
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