Print

Print
Dear Joao,

>So, my questions are: At the end, you just need to smooth the "mwrp1*-affine.nii" images and do the stats? These "mwrp1*-affine.nii", as well as the smoothed versions and the results are in MNI space?

Yes, as long as the images are written out in rp*-affine space. DARTEL 'create Template' warps the images to their average anatomy (the DARTEL-templates 1-6), and the average anatomy of x images linearly (12-parameters, affine transform) aligned to MNI space will also be in MNI space.
If you write the images as rp*-rigidly aligned to MNI space (SPM default) in the VBM8 toolbox, then your images are just rotated and translated (3 +3 = 6 parameters) to match the --orientation-- of MNI space. They are not scaled and thus do not conform to MNI space and will not after DARTEL-registration using 'create Template' and 'create warped'. These images can be warped with 'create Template' and subsequent 'Normalise to MNI space', i.e. VBM8 segmented images rigidly aligned to MNI space can be used the same way as DARTEL imported images from SPM8-New Segment (or even 'old' segment + DARTEL import).

Best,
Michel 

Date: Thu, 2 Dec 2010 17:42:14 +0000
From: [log in to unmask]
Subject: Re: [SPM] Fwd: [SPM] VBM8 quesiont
To: [log in to unmask]

Dear Michel and Tanja,

I've been following your very useful discussion.

I have a couple of related questions more:

If you use the VBM8 "Estimate & Write" module to do segmentation, you can get the DARTEL formatted "rp*-affine.nii" tissue classes. In the VBM8 manual (page 18) you can read that with the Estimate & Write module "The volumes “rp1*‐affine.nii” and “rp2*‐affine.nii” will be written. These are the grey (rp1) and white
(rp2) matter segments after an affine registration to the MNI template". After that it is only suggested to run only the Modules "Run DARTEL (create Templates)" with "rp*-affine.nii" input, and finally the "Create warped" with flow fields "u_*.nii" and "rp*-affine.nii" inputs. This "Create warped" module has the option to "Preserve Amount (Modulation)".
Also in the beggining of this page you can read "This option uses affine registered GM and WM segments and modulates the segmentations for nonlinear
effects only, which accounts for brain size. No additional normalization to MNI space is
necessary, because the DARTEL template is provided in that space."

So, my questions are: At the end, you just need to smooth the "mwrp1*-affine.nii" images and do the stats? These "mwrp1*-affine.nii", as well as the smoothed versions and the results are in MNI space?

Thanks for your help,

João Duarte



On Thu, Dec 2, 2010 at 3:31 PM, michel grothe <[log in to unmask]> wrote:
Dear Tanja,
1. An absolute Threshold of 0.2 is totally acceptable and much more common than 0.01. Alternatively you can apply a brainmask for analysis (e.g. see Ridgway et al, 2009; http://www.ncbi.nlm.nih.gov/pubmed/18848632).
2. DARTEL 'Create Template' high-dimensionally registers your subjects to their average-anatomy, represented by Template_6. This template will most probably differ from MNI space (Normal brains are on average smaller than the MNI-template). This is why DARTEL 'Normalise to MNI space' estimates an (12-parameter) affine transform from Template_6 to MNI space and combines this transform with the individual DARTEL flow-fields. The scheme is:
Native --DARTEL--> Template_6 --affine--> MNI Template, where the last transform is the same for each subject and aims to model global brain size (and shape) differences between the average anatomy of your specific group and the MNI Template.
Your Template_6 will not be transformed to MNI space, which is why you see the disagreement with your results, which are derived from your warped tissue-classes in MNI space.
 
The best would be to overlay your results on a template based on the images you used for the stats, that is an average of your warped tissue-classes (or warped structurals as explained in my previous mail). You can use imcalc for this: Expression: mean(X); Options: Yes, read images in data matrix (--> X). This template can be considered something like 'average anatomy of the group in MNI space' and best matches the space of your results.

BTW, the avgT1_Dartel_IXI550_MNI152.nii is specific to the VBM8-toolbox and is not an official MNI template (although given that it is based on an average of the normal population aligned to MNI space, it should be very similar to MNI152, which is the most widely used official template of MNI space).

Hope this helps,
Michel

> Date: Thu, 2 Dec 2010 14:42:28 +0100

> From: [log in to unmask]
> Subject: Re: [SPM] Fwd: [SPM] VBM8 quesiont

> 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.
> >>> >
> >>
> >