On 02/06/2013 12:49 PM, Gabriel Gonzalez Escamilla wrote: > Dear Doug and FreeSurfer experts, > > Thnak you so much for all your lasts responses!. > > I did ran succesfully all the pre-processing for the interhemispheric > comparisons on FS. Now I have a couple questions: > > given the command for interhemispheric comparisons: > mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir > glm.lh.lh-rh.thickness.sm05 --osgm --surf fsaverage_sym lh; > > A) This read all subjects to construct X and C as one-sample group > mean, this means that as result I get the difference across > hemispheres and across my subjects in a population, right? Correct. > > B) But, what if I have two groups? controls and patients, I'm > wondering if is it possible to examine regional differences of > thickness asymmetries between those two groups? or more? This just becomes a standard two group analysis as described in the tutorials. You create an FSGD file with two classes and list your input subjects. > > C) If I want to examine effects of group or sex, while controlling for > age and other factors how do I introduce them into the glm model? If > so, do I set the contrasts as normally for mri_glmfit? I mean as any > other thickness study? or there is any other thing that I should do? You do not need to do anything different than with a normal thickness study. > > The command for multiple comparisons correction is: > mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 > Which performs only cluster-wise corrections, > > D) is there any other way to correct for multiple comparisons, > something like permutation tests or anything else? Yes, you can run something like mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 --sim perm 10000 2 csdperm --sim-sign abs You should run mri_glmfit-sim --help to see what these options mean as you may need to change the voxelwise threshold (the "2" value)
doug > > > Many thanks in advanced, > Gabriel -- 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: 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.
