> To:
[log in to unmask]>
> Dear all,
>
> I also wanted to note that for Factorial design specification I use
> Threshold masking -> absolute threshold 0.01. I tried higher values,
> it gives better results if threshold is 0.2 (but only while
> overlapping the statistics on any MNI template, not Template_6.nii).
>
> Therefore, I have 2 questions.
>
> 1. Is threshold of 0.2 considered too high or acceptable?
> 2. The Template_6.nii is smaler than any MNI template, so is it or is
> it not normalized to MNI at step "Run DARTEL (Create Templates)"?
>
> Thank you,
> Tanja.
>
>
> On Thu, Dec 2, 2010 at 1:17 PM, Tetiana Dadakova <
[log in to unmask]> wrote:
> > 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. You´d 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 don´t 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.
> >>> >
> >>
> >