Thanks Doug. After using stage#1 of the longitudinal 2-stage model to create cross-sectional measuers of e.g. thickness change from tp1 to tp2 (e.g. thickness-pc1), I then did analyses in QDEC on these measures to see where in the brain such changes are
- different from zero (within each group); and - different between groups (for every pair of groups in the current qdec table, e.g. F vs P) For thickness-pc1 it all went fine, but for area-pc1 analyses, I get this error right after starting the MonteCarlo Null-Z correction: "Completed loading of analyzed data. fwhm.dat: 8.654965, rounded to 9. ERROR: CSDread(): could not open /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm9/abs/th13/mc-z.csd". This happens regardless of the threshold used (e.g. 0.01 or 0.05) In case it's relevant, for the thickness analyses (whose correction worked fine), the fwhm.dat was "10.190419, rounded to 11". I am using FS 5.3.0 (Ubuntu). Thanks! Tudor On 17 June 2014 09:29, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > It only needs to be accounted for when you compare across all 3 groups, in > which case you'd have to use mri_glmfit > doug > > > > On 6/17/14 12:07 AM, Tudor Popescu wrote: > > Hi Doug, > > Thanks... Presumably I'd just leave each possible pair of groups at a time > in the qdec table, and delete rows corresponding to subjects of the > remaining group? And then do stats on, e.g. "long.thickness-rate" to > compare rate of change between the current pair of groups? > Doesn't variability across all 3 groups somehow have to be accounted for? > > Tudor > > > On 16 June 2014 20:38, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > >> >> Yes, you could do each separately. >> doug >> >> >> >> On 6/16/14 8:10 PM, Tudor Popescu wrote: >> >> Dear FS list, >> >> I have a data set with 3 groups (2 treatments, 1 control), each with >> equally-spaced time-points (pre and post structural scan). I've done the 3 >> longitudinal pre-processing steps, and stage#1 of the two-stage model, and >> I would prefer to run stage#2 (cross-sectional analysis of the difference) >> with QDEC as opposed to with mri_glmfit. >> >> I know that QDEC is meant for 2 groups, but I see that designs with 4 or >> 6 groups can be analysed with QDEC (as per this >> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples> FSGD examples >> page) whereas designs with 3 groups cannot be. It seems to me that an even >> number of groups is QDEC-able while an odd number isn't, but is there any >> workaround so that I can still use QDEC? Perhaps if I only do pairwise >> comparisons one at a time, i.e. treatment1 vs control and treatment2 vs >> control? >> >> Many thanks! >> Tudor >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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