On 04/29/2013 04:13 PM, Tudor Popescu wrote: > Dear Freesurfers, > > I am doing an ROI analysis (group comparison) of cortical thickness, > and I have some questions that I could use some help with. Many thanks > in advance! > > Tudor > > 1) I used aparcstats2table to extract CT values for structures from > the Destrieux atlas, but I cannot identify some important cortical > structures among the names in that list. For example, I don't see > anything corresponding to the Superior Parietal Lobule, or the > Intraparietal Sulcus (the latter actually does appear but is coupled > with another structure, under the name > "lh_S_intrapariet_and_P_trans_thickness") Have you looked in Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature Christophe Destrieux, NI, 2010?
> > 2) Can the same table (of the average CT of each cortical > parcellation) be extracted using parcellations based on an atlas other > than the Destrieux (e.g. the Harvard-Oxford, or the Julich)? There is nothing automatic do to it, but if you have those atlases mapped to the individual, you can create a color table (like FreeSurferColorLUT.txt) and run mri_segstats then asegstats2table > > 3) (I can't see whether there's a tutorial for this, as the main FS > site seems to be down at the moment) How can a group comparison of CT > be done inside a given ROI, and in what ways can the ROI be specified? > I guess the command line version of QDEC would produce, in this case, > the same contrasts as QDEC, but within the ROI as opposed to the whole > brain You mean you want to do an exploratory analysis within a mask of an ROI or that you want to average the CT scan within the ROI and do a group analysis of the ROI values? If the former, you can use mri_glmfit with the -label or -mask option. If the latter, you can create a table with asegstats2table then run mri_glmfit with --table > > 4) How do the results of these two different types of ROI group > analyses differ, and is one of them more "correct" than the other: > A) running the command prompt version of QDEC within the confines > of a certain atlas-defined ROI, and looking at the resulting > statistical map (clusters), as per question 3; > B) extracting the CT values for that ROI for all subjects using > aparcstats2table, and doing t-tests to look for a group difference. Oops, looks like these are the two I mentioned from #3 above. The first is an exploratory analysis in which the groups are compared on a vertex-by-vertex basis. If there is a subset of vertices that are different between the groups, it may show up in the exploratory analysis. However, the effect may be small at each vertex and averaging over the vertices may improve your power (unless the effect is only at a few vertices). One is not more correct than the other, just testing different hypotheses. doug > > _______________________________________________ > 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.
