Dear John and SPMers,
I am facing a problem while performing DARTEL-based normalization of my
fMRI data followed by group analysis.
I followed the below routine to conduct first level and second level
analysis on my fMRI data:
(1) coregister fMRI and structural for each subject
(2) perform DARTEL among segmented structural data
(2) use the code provided by John to transfer both fMRI and structural
data to DARTEL space
(3) perform first-level analysis of the fMRI data --> output: con files
(4) in order to perform second level analysis, I apply DARTEL parameters
to warp my con files (using "create warp").
The problem is at step 4: the warped con images seems not to have
correct orientation. However, if I apply the same parameters to the fMRI
data that are transformed to DARTEL space (from step 2), the data look OK.
Is there anything that I am missing?
Thank you,
Regards,
Amir
John Ashburner wrote:
> This will be straightforward in SPM8 - and it will combine the transforms with
> an affine transform so that the spatially normalised images are in MNI space,
> rather than the population average. SPM8 will be released very soon, but I
> think the necessary routines are already available in the recent updates for
> SPM8b.
>
> An alternative strategy could be to spatially normalise contrast images from a
> first level analysis done in native space, prior to doing the 2nd level
> analysis. This could be done one scan per subject.
>
> Best regards,
> -John
>
> On Monday 30 March 2009 17:24, Amir Tahmasebi wrote:
>
>> Dear John,
>>
>> I am using DARTEL to warp fMRI data. Using DARTEL's "create warped"
>> tool, for every image you have to provide one flow field. Is there any
>> way that I can apply one flow field to a bunch of images at once?
>>
>> Thank you,
>>
>> Regards,
>> Amir
>>
>> John Ashburner wrote:
>>
>>> DARTEL is run as described in the user guide, but there is an extra
>>> option that allows the resulting deformations to be automatically
>>> combined with an additional affine transform. The DARTEL warps encode
>>> the inter-subject variability, and the affine transform warps the average
>>> of the population to MNI space.
>>>
>>> Best regards,
>>> -John
>>>
>>> On Tuesday 24 March 2009 17:49, Amir Tahmasebi wrote:
>>>
>>>> Hi John,
>>>>
>>>> Thanks for your reply.
>>>>
>>>> Does this mean that the fMRI data are only affinely registered between
>>>> subjects?
>>>>
>>>> Regards,
>>>> Amir
>>>>
>>>> John Ashburner wrote:
>>>>
>>>>> If you have SPM8b (latest updates), then you should find this much
>>>>> easier, as there is now an option to spatially normalise (and spatially
>>>>> blur) fMRI to MNI space (as it incorporates an additional affine
>>>>> mapping between DARTEL template and MNI template). I haven't had a
>>>>> chance to update the user guide for DARTEL yet, but it should be
>>>>> reasonably straightforward to use.
>>>>>
>>>>> I expect that the t stats should be increased, and look forward to any
>>>>> feedback on whether this is the case.
>>>>>
>>>>> Best regards,
>>>>> -John
>>>>>
>>>>> On Tuesday 24 March 2009 16:22, Amir Tahmasebi wrote:
>>>>>
>>>>>> Dear John and SPMers,
>>>>>>
>>>>>> I am trying to use DARTEL for normalization of fMRI data. I have
>>>>>> looked at "how to use DARTEL for normalizing fMRI con maps?" thread
>>>>>> but it is not exactly what I was looking for.
>>>>>>
>>>>>> I was wondering how should I use the outputs of DARTEL ("u_rc1*.nii"
>>>>>> and "Template_6.nii") to normalize my fMRI data which is already
>>>>>> coregistered to the corresponding structural data.
>>>>>>
>>>>>> Thank you,
>>>>>> Amir
>>>>>>
--
________________________________
Amir M. Tahmasebi
Ph.D. Candidate,
Medical Image Analysis Lab.
School of Computing,
Queen's University,
Kingston, Ontario
CANADA
K7L 3N6
________________________________
Tel: (613) 533-2797
Web: www.cs.queensu.ca/~tahmaseb
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