Hi again, I've looked into mri_glmfit-sim --help to figure out which files I could overlay in tkurfer after correcting for multiple comparisons using the instructions for xhemi on the freesurfer wiki. However, I do not see any of these files (csd.base...) in the glmdir/osgm folder. I only see ones that begin with cache..... Are these the files I should be overlaying? Or should I be using different commands for my analyses?
here is the command line I used: mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ --cwpvalthresh .5 --cache 2 abs Prior to mri_glmfit, I conducted the "create a stack of subjects" using paired-diff-norm in place of paired-diff Ultimately, I want to look at hemisphere asymmetries (preferably in terms of laterality indices) in two different groups separately. I would also like to see if laterality indices differ between groups. Is this possible? Thanks! Krista On Mon, Dec 9, 2013 at 4:00 PM, krista kelly <krista.kell...@gmail.com>wrote: > Great Thanks! > > > > > On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> >> On 12/09/2013 11:53 AM, krista kelly wrote: >> > Thanks Doug! I'll try that instead. >> > >> > Also, do you or anyone else happen to have the answers to my other >> > questions (reposted below): >> > >> > 1) When viewing the results in tksurfer, which color represents "left >> > hemisphere is larger" and which represents "right hemisphere is larger"? >> If you are just doing a simple interhemispheric difference, then >> yellow/red will be left>right and blue left<right >> > >> > 2) I have no idea how to view the results in tksurfer AFTER performing >> > the step of correcting for multiple comparisons. Any suggestions? >> >> If you run mri_glmfit-sim with --help you will see a list of output >> files with descriptions for each. Choose the one you want and run >> tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay >> csdbase.sig.cluster.mgh ) >> >> doug >> >> > >> > Thanks! >> > Krista >> > >> > >> > >> > >> > On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > Run mris_preproc with --paired-diff-norm which will then compute >> > LI = (L-R)/(.5*(L+R)) >> > Note that some people use >> > LI = (L-R)/(L+R) >> > If that is what you want, then divide the mris_preproc result by 2 >> > >> > doug >> > >> > On 12/08/2013 08:45 PM, krista kelly wrote: >> > > Hello, >> > > >> > > I'm analysing interhemispheric differences using xhemi. I have >> > > followed the instructions on the webpage with no problems. I do >> > have a >> > > few questions though. >> > > >> > > 1) When viewing the results in tksurfer, which color represents >> > "left >> > > hemisphere is larger" and which represents "right hemisphere is >> > larger"? >> > > >> > > 2) I have no idea how to view the results in tksurfer AFTER >> > performing >> > > the step of correcting for multiple comparisons. Any suggestions? >> > > >> > > 3) I've noticed from the archives that some people are performing >> > > laterality indices. How would I calculate laterality indices? >> > > >> > > Thanks! >> > > Krista >> > > >> > > >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> > Fax: 617-726-7422 <tel:617-726-7422> >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://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 <mailto: >> 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. >> > >> > >> > >> > >> > _______________________________________________ >> > 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 >> > >
_______________________________________________ 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.
