Dear Prof. Greve I have additional (and probably silly) questions.
1) Is there much difference between result of monte-carlo null-z simulation (QDEC GUI) analysis and that of clusterwise correction for multiple comparisons using 10000 permutations? I'm guessing similar results between both methods; however I'm wondering whether significant clusters from the former processing might disappeared when using the latter process, or vice versa? 2) Does QDEC analysis automatically produce *.glmdir files for each contrast? If not, how can I make *.glmdir from the QDEC (not using the mri_glmfit command)? Thank you for your kindness Kim 2013/7/9 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > > On 07/07/2013 01:36 PM, jh kim wrote: > > Dear FreeSurfer experts... > > > > Please be patient with a newbie's questions. > > For the first time, I'm trying to analyze between-group differences in > > cortical thickness (controls vs. patients) by using FS 5.1.0 and QDEC. > > I've read through the online manual and mailing lists; however, I > > cannot figure out the following queries. > > > > 1) I selected 'group' (con, pat) as a fixed factor (gender is not > > applicable because all are females), and demeaned age as a continuous > > covariate. After analyzing using DODS option, several questions are > > shown in the Display GUI panel. Does the question "Does the average > > thickness differ between con and pat?" mean between-group difference > > of cortical thickness after *controlling for the effect of age*? > Yes, it controls for all your other factors. > > > > 2) Should I include average cortical thickness of the left or right > > cortex (calculated from the command, mris_anatomical_stats -l > > lh.cortex.label -f subid.txt subid lh)as a nuisance variable? I know > > this issue has been addressed many times before, and it is generally > > recommended not to include as a nuisance factor. However, in case of > > statistically significant difference in mean cortical thickness of one > > hemisphere (unpaired two sample t-test by SPSS), is it still not > > necessary to include it as a nuisance factor? From the similar points > > of view, how about volume and surface area analyses (include or not > > total cortical volume and total surface area as a nuisance factor, > > respectively) ? > I don't have a strong opinion about removing the global mean thickness, > but I think others (Mike Harms?) recommend to do so. For volume and > surface area, you probably want to normalize by the ICV. > > > > 3) I found several significant clusters that are corrected for > > multiple comparisons using Monte Carlo simulation (corrected P < 0.01) > > in the bottom of Display panel. I assume that this procedures take > > 10,000 permutations by default. Am I right? > It is 10k iterations of generating white noise (not a permutation test > unless you specified that explicitly). > > > > 4) Last question, how can I extract individual value (cortical > > thickness per subject) from the significant clusters? I want to do > > this 'all-at-once'. Please let me know the command. > There should already be a file in the output folder called > something.y.ocn.dat that has a row for each input subject and a column > for each cluster. > doug > > > > Apology for bothering you. > > Any comments would be greatly appreciated. > > > > Thanks. > > Kim > > > > > > _______________________________________________ > > 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 > > > 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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