Hi John,
I used the "import_for_dartel.m" file from another posting dated on Wed.
6 Feb. 2008.
Regards,
Amir
John Ashburner wrote:
> I'm not quite sure what you mean by " use the code provided by John to
> transfer both fMRI and structural data to DARTEL space". If this means using
> the create DARTEL warped images, then then doing this again to the contrast
> images (step 4) is going to move the data out of alignment.
>
> If you have SPM8b (soon to be SPM8), then maybe try skipping the "use the code
> provided by John" step. Generate the contrast images in native space
> (without smoothing), and simply warp them using the new "Normalise to MNI
> space" option of DARTEL.
>
> Best regards,
> -John
>
> On Wednesday 01 April 2009 18:24, you wrote:
>
>> 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
