Dear Michel,
thank you for your answer. I tried to do just 3 steps, according to
your mail. It looks a little better, but still something is wrong with
template.
In the attachment you can see the statistics overlaid on the Template6.nii.
Do you have any idea what can be the problem, at which step can I make
a mistake?
The steps:
0. Reorient all the images to AC-PC line (most of images are .nii, but
some are .img/.hdr)
1. Segmentation: Tools -> New Segment
2. DARTEL Tools -> Run DARTEL (Create Template) (input: rc1*.nii,
rc2*.nii, rc3*.nii)
3. DARTEL Tools -> Normalize to MNI space (input: u_rc1*.nii, Template6.nii)
4. Factorial design specification (2 sample t-test, covariates: age,
tissue volume)
Thank you,
Tanja.
On Fri, Nov 26, 2010 at 9:26 PM, michel grothe <[log in to unmask]> wrote:
> Dear Tanja,
> there is a problem wit your processing steps. YouŽd normally directly warp
> the images to MNI space, i.e. omit steps 3 and 4. The "Normalize to MNI
> space" option in SPM8 estimates an affine transform from the DARTEL template
> (specify your DARTEL-template_6 here) to the MNI-template and combines it
> with the individual DARTEL flow-fields to warp each subject directly from
> native space to MNI-space (better "average anatomy of your sample in MNI
> space"). Step 3 and 4 had to be used in SPM5 but are not necessary anymore
> in SPM8. The "create warped"-option is only for the case you donŽt want to
> normalise to MNI space (but to the pure average anatomy of your sample).
>
> Best,
> Michel
>
>> Date: Fri, 26 Nov 2010 16:33:18 +0100
>> From: [log in to unmask]
>> Subject: [SPM] VBM8 quesiont
>> To: [log in to unmask]
>>
>> Dear SPM list,
>>
>> I have a problem with VBM8 data processing. When I try to overlay
>> statistics on the template (wTemplate6.nii), it seems that the
>> template is either shifted or the size of the template doesn't
>> correspond (the significant clusters are supposed to be in gray matter
>> region, see attached image).
>>
>> 1. Could you please explain to me what can be the problem? Can it be
>> the problem of wrong template generation or of statistical
>> calculations?
>> 2. At which of the following step is the smoothing done?
>>
>> Here are the steps I take
>> 1. Segmentation with Tools -> New Segment
>> 2. Creating DARTEL template Template6.nii with Tools -> DARTEL Tools
>> -> Run DARTEL (create Templates)
>> 3. Normalizing Template6.nii to MNI with Spatial -> Normalise:
>> Estimate & Write (get wTemplate6.nii)
>> 4. Warping segmented images with Tools -> DARTEL Tools -> Create Warped
>> 5. Normalizing warped images to MNI with Tools -> DARTEL Tools ->
>> Normalize to MNI Space (using wTemplate6.nii here)
>>
>> Thank you for your time,
>> Tanja.
>
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