yes, it is just like a "normal" group analysis. You create a stack of LI maps, one for each subject, create an FSGD file, run mri_glmfit, then mri_glmfit-sim.
doug On 01/13/2014 06:22 PM, krista kelly wrote: > > Just wanted to repost this in case anyone else can give some advice. > Thanks! > > Is there any way to analyze group differences with xhemi? I can get > the laterality indices per group, but I'd like to do a whole brain > analyses looking at group differences in laterality indices. > > Thanks, > Krista > > > On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > Yes, use the cache files. When "--cache" is used, the csdbase="cache" > > On 12/10/2013 12:20 PM, krista kelly wrote: > > 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 <mailto:krista.kell...@gmail.com> > > <mailto:krista.kell...@gmail.com > <mailto:krista.kell...@gmail.com>>> wrote: > > > > Great Thanks! > > > > > > > > > > On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto: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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > > > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > > <http://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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > > <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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > 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 > > > > > > _______________________________________________ > 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
