On 11/06/2017 12:03 PM, lanbo Wang wrote: > Dear experts, > > I have two questions about hemisphere analysis: > > 1) When I run left-right hemisphere paired t-test, can I add age as > covariate? If use fsgd to add covariate, to this paired t-test > analysis, how to make the fsgd table? use this one-group, one-covariate example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V > 2) I want to reorganize the hemisphere from left-right to > symptom-nosymptom according to body symptom side record and compare > different between symptom hemisphere and nosymptom hemisphere. Can I > use freesurfer to do it? Yes, though it is a little tricky with multiple ways, each complicated in its own way. 1. Create your own design matrix. You can use the one created by mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then, in each subject whose symptomHemi is rh, multiply its line in the design matrix by -1. Then pass this design matrix to mri_glmfit with --X instead of passing an FSGD file. 2. Load the output of mris_preproc into matlab, eg, y = MRIread('y.mgh');, then change the sign as in #1 above, eg, y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run mri_glmfit as normal with the new file. 3. Run mris_preproc for each subject separately to generate an lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in #1 above with fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o lh.lh-rh.thickness.sm00.subject10.mgh Then run mri_concat to concatenate all the subjects together in the same order as they are listed in the FSGD file, then use this stack as input the mri_glmfit
> > Thanks for your patient and help. > > All best, > Lanbo Wang > > > _______________________________________________ > 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.
