This is a bug in QDEC. I'm surprised it has not surfaced before. It is supposed to be looking in "fwhm09" not "fwhm9". One work-around is to create a symlink, ie,
cd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/ ln -s fwhm09 fwhm9 otherwise, you will have to run mri_glmfit-sim doug On 06/20/2014 11:48 AM, Tudor Popescu wrote: > 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 > <mailto: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 >> <mailto: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 list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto: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 list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
