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Thanks Karl, Jack, Thanks for getting back to me. Masking using the segmented cortex as a template does sound like an interesting proposition - and perhaps more valid than a post-hoc ROI analysis. Though I do have some ideas about which areas might show a BOLD response, I was just having an initial "look see" at the data using random effects. Prior to performing the random effects (RE) analysis, I had a look with fixed effect (FE) analysis - which gave several significant areas of activation (corrected-p). The finding that these areas vanished with the RE analysis wasn't unexpected, but when I dropped the significance level I didn't obtain the same pattern of activation (as in the FE analysis). Is this to be expected? I guess it may have been a consequence of the FE results being biased by a single subject (?) - or am I missing the point? Is there a good reference for RE/FE analysis? Thanks again, Jon. _____________________________________________________ Jonathan Brooks Ph.D. (Research Fellow) Magnetic Resonance and Image Analysis Research Centre University of Liverpool, Pembroke Place, L69 3BX, UK tel: +44 151 794 5629 fax: +44 151 794 5635 On Sat, 3 Jun 2000, Foucher Jack wrote: >Dear Jon, Karl and others > >> >> Dear Jon, >> >> > I have recently been experimenting with a random effects analysis of >> > several trials in an fMRI study. I have 18 subjects, so I guess this is >> > the right analysis to use. Basically, I was wondering whether I should >> > use a corrected height threshold in the generation of the SPMs? If I do >> > I get no supra-threshold clusters. >> > >> > Is it appropriate to use an uncorrected p, given that the random >> > effects analysis is quite stringent? Is there any general consensus on >> > the best approach to choosing p-levels in this situation? >> >> I am afraid exactly the same inference criteria apply to first and >> second level analyses. I would think about any anatomical priors that >> could be used to provede small volume correction to the p values. One >> point you might want to take forward is that inter-subject differences >> may include anatomical variations in the response profile. Increasing >> the smoothing (of the con??? or beta???.img) prior to the 2nd level >> analysis might improve your sensitivity (e.g. 8mm FWHM). >> >> I hope this helps - Karl > >I hope that the following proposition won't seems to odd ! > >Let say that you have no clear idea of which cortical region should activate >except that you are looking for cortical activation only. >Why not using a mask constructed on the basis of gray matter segmentation for >corrected p ? >You will just have to choose a threshold from your gray matter segmentation map >in order to put the above values to 1 and the others to 0. Than you could >eliminate the basal ganglia by a logical routine setting to 0 every voxel >between a certain coordinate. >I tried this approach once just for testing the feasibility, and it allowed me >to use less conservative threshold (although the gain was not proportional to >the volume loss - see Matthew's pages on SVC for reasons to that). > >Does this sounds reasonable ? Did anyone else tried this, and what difficulty >did they have to cope with ? The most critical point I faced was the threshold >do use (as far as I remember, 200 seems to be resonable). Any advice on that >point ? > >Since I did try this at the time of SPM99 beta and using Matthew's SVC routines >(that gave the uncorrected p to use for equivalent corrected p), I faced a >problem of representation : how to display the only activation falling within >the mask (except by removing them 'by hand' from the T.img using the same mask >- I haven't tried that) ? > >Thanks for any input >Sincerely > > > >Jack > >_________________________________________________________________ >| Jack Foucher Universite Louis Pasteur | >| Institut de Physique Biologique UPRES-A 7004 du CNRS | >| 4 rue Kirschleger Tel: 33 (0)3 88 77 89 90 | >| 67085 STRASBOURG Fax: 33 (0)3 88 37 14 97 | >| France | >| Faster E-mail: [log in to unmask] | >| Other [log in to unmask] | >|_______________________________________________________________ | > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%