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.
