Hi Maria, how did you extract the thickness for each subject? mri_glmfit-sim will do this extraction for you. It will be stored in something.y.ocn.dat. Try it with that data. Also, how did you do your GLM analysis? Did you use the Xg.dat file created by QDEC? doug
On 07/23/2013 11:48 AM, Maria Kharitonova wrote: > Hi, I'm sorry for sending a duplicate request, but I am still really > confused about the discrepancy between group-level findings in qdec > (ROIs that are different across my 2 groups) and lack of a difference > on the extracted thickness measures for those same custom ROIs. More > info is below. Please let me know if you have any insight about this > discrepancy. Thanks in advance! > > ---------- Forwarded message ---------- > From: *Maria Kharitonova* <maria.khariton...@colorado.edu > <mailto:maria.khariton...@colorado.edu>> > Date: Thu, Jul 18, 2013 at 4:32 PM > Subject: qdec -- confused by glm output for custom ROIs > To: freesurfer <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > > Hello, > > I have a question regarding the interpretation qdec's output for the > custom ROI's thickness estimates. I ran an analysis comparing cortical > thickness in children with and without ADHD (categorical variable), > controlling for age and demeaned ICV, using 5.0. After controlling for > multiple comparisons with the monte-carlo simulation, there were 2 > ROIs in the right hemisphere that were significantly different across > groups: a regions near parstriangularis and near medial orbital > cortex. I then created custom ROIs for these regions, and extracted > thickness estimates for each participant for each of these ROIs. > > I then decided to do a "sanity check" of the data -- run a linear > regression on these extracted thickness estimates to see if the mean > thickness in each region differed as a function of diagnosis (again > controlling for age and demeaned ICV). By logic, I should see > differences in thickness estimates for these 2 ROIs across the 2 > groups, because that's how these ROIs were defined, right? But in > reality, there is no difference at all between groups, with p-values > around .9! > > I tried saving the ROIs by both manually tracing and with the > mri_surfcluster command -- I get very similar estimates of thickness > (correlation coefficients of .9 across 32 subjects). So that's not the > cause of error. Both manual and automatic extraction fails to find > differences across subjects that I described above. > > What am I missing? is the original GLM in QDEC that finds differences > between groups doings something other than looking for differences in > each voxel/region across groups? > > Thanks in advance for the help! > Maria > > ******************************* > > Maria Kharitonova, Ph.D. > Postdoctoral Research Fellow > Laboratories of Cognitive Neuroscience > Boston Children's Hospital > Division of Developmental Medicine > Harvard Medical School > > > > _______________________________________________ > 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.
