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SPM  December 2010

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Subject:

Re: Fwd: [SPM] VBM8 quesiont

From:

Tetiana Dadakova <[log in to unmask]>

Reply-To:

Tetiana Dadakova <[log in to unmask]>

Date:

Thu, 2 Dec 2010 13:17:49 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (125 lines) , spm_quest_mni.tiff (125 lines)

Dear Michel,

thank you for your reply.

In attachment you can see statistics overlaid on template
avgT1_Dartel_IXI550_MNI152.nii. It is better, but still not good
enough. (Is it the MNI template you mentioned or is there other
standard MNI template in SPM?)

I am a bit confused about the Template6.nii. It is written in VBM
Tutorial by John Ashburner (this one
http://www.fil.ion.ucl.ac.uk/~john/misc/VBMclass10.pdf) that
"...Template 6.nii. This template is registered to MNI space (affine
transform), allowing the transformations to be combined so that all
the individual spatially normalised scans can also be brought into MNI
space."
Therefore, if I understand correctly, Template6.nii is in MNI space, right?

Thanks again, I appreciate your help,
Tanja.




On Thu, Dec 2, 2010 at 12:30 PM, michel grothe <[log in to unmask]> wrote:
> Dear Tanja,
> I suppose that the template in the attached image is your DARTEL-Template6.
> This would explain the mismatch of the overlayed results, which are in MNI
> space (The MNI template brain is a bit bigger than average anatomy). Try
> projecting them on a standard MNI-template or create your
> 'group-specific'-MNI-template by warping and averaging the structurals using
> 'Normalize to MNI space' (input: u_rc1*, T1-structurals, Template6; no
> modulation, no or only small smoothing).
>
> Hope this helps,
> Michel
>
>> Date: Wed, 1 Dec 2010 20:38:58 +0100
>> From: [log in to unmask]
>> Subject: [SPM] Fwd: [SPM] VBM8 quesiont
>> To: [log in to unmask]
>>
>> 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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