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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