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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. > >