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SPM  May 2009

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Subject:

Re: R: [SPM] Longitudinal DARTEL spm8

From:

John Ashburner <[log in to unmask]>

Reply-To:

John Ashburner <[log in to unmask]>

Date:

Fri, 22 May 2009 11:58:00 +0000

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The suggestion I made was about how to use DARTEL to do the intra-subject 
alignment, so I was basically just answering the question.  I have no 
empirical evidence either way, but (for the reasons I mentioned) I suspect 
that HDW may do a marginally better job with most serial scans.

Best regards,
-John

On Friday 22 May 2009 11:15, Benetti, Stefania wrote:
> Thank you John for your answers and suggestions. However, I am not sure to
> understand what you are suggesting about HDW approach that Kipps used.
>
> "In general, I think I would still suggest the HDW approach that Kipps and
> others have used...For inter-subject alignment, the residuals are rarely
> i.i.d. Gaussian, which is why I chose to align tissue class data
> instead.... However, the segmentation errors may be relatively large
> compared with the volumetric differences between the serial scans, which
> would make the DARTEL approach less accurate"
>
> My understanding was that the procedure you suggested to Reinders
> (https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0804&L=SPM&P=R48484)
> consisted in an adaptation of Kipps' approach for DARTEL, in which the
> within subject alignment approach replaced the HDW. Am I completely wrong?
> Did you mean that this longitudinal DARTEL procedure may be less accurate
> than the procedure that Kipps actually used?
>
> Many thanks again
> Stefania
>
>
> -----------------------------
>
> Stefania Benetti
> King's College - Institute of Psychiatry
> Neuroimaging Section
>
>
>
>
> -----Messaggio originale-----
> Da: John Ashburner [mailto:[log in to unmask]]
> Inviato: gio 21/05/2009 13.50
> A: Benetti, Stefania; [log in to unmask]
> Oggetto: Re: [SPM] Longitudinal DARTEL spm8
>
> > We pre-processed a small longitudinal dataset (26 subjects,T1=baseline
> > T2=follow-up) using DARTEL and the procedure suggested in:
> >
> > https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0804&L=SPM&P=R48484
> >
> > Briefly,
> > a) both T1 and T2 manually reoriented. T2 co-registered to T1,no
> > re-slicing. b) segmentation of  both T1 and T2 images (section 1.1 DARTEL
> > manual). c) create within-subject template (smoothing parameter to NONE)
> > d) generate modulated warped GM an WM using the within-subject flow
> > e) create an inter-subject template
> > f) generated modulated warped(mwmwc1T1 and mwmwc1T2) GM and WM using the
> > inter-subject flow fields. g) smoothing and statistical analysis using
> > both a flexible factorial design.
> >
> > However  when we pre-processed the same database using optimised VBM for
> > serial scans and then the same statistical analyses, we obtained a
> > completely different result. GM changes were found in regions where no
> > significant effects were detected with the DARTEL approach.
> >
> > Would you expect to find such a difference?
>
> I would expect different models to give different results, so I'm not
> really surprised.  I would suggest checking out the contrast images
> generated from the GLM to see if the general trends are similar.
>
> > Could this difference in terms
> > of localisation be attributable to differences in normalisation?
>
> Very likely, and also differences in tissue classification.
>
> > Is it
> > sensible to rely on the DARTEL approach rather than the optimised one?
>
> I haven't tested the various approaches to know what works "best", and the
> most sucessful approach is likely to be dependent on things like the
> contrast in the images, the image artifacts and the stability of the
> scanner. However, I would expect that some form of within subject alignment
> approach may provide more sensitivity to differences.  For longitudinal
> analyses, you are identifying tiny volumetric differences of the order of a
> percentage or so, so the details really do matter.
>
> In general, I think I would still suggest the HDW approach that Kipps and
> others have used.  There are issues with HDW, which relate to the algorithm
> fully converging and it is also asymmetric (so registering early with late
> will give different results from doing it the other way around), but it is
> probably the more accurate of the SPM procedures to use for longitudinal
> studies. A histogram of the difference between the registered images should
> approximately indicate that the residuals are i.i.d. Gaussian, which would
> make the mean-squares difference (used by HDW) a suitable objective
> function to use.  For inter-subject alignment, the residuals are rarely
> i.i.d. Gaussian, which is why I chose to align tissue class data instead. 
> However, the segmentation errors may be relatively large compared with the
> volumetric differences between the serial scans, which would make the
> DARTEL approach less accurate.
>
> > One more question about step d) in the procedure mentioned above. Is this
> > step necessary? I am probably missing something, but I was wondering if
> > warping the T1 and T2 images using the within-subject flow fields, and
> > then warping the obtained images again with the inter-subject flow fields
> >  (step f) may reduce local differences we are actually interested in
> > since we are dealing with serial scans.
>
> The transforms could be composed and then used, but I'm not sure how much
> difference it would make in practice.
>
> Best regards,
> -John

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