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>> 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>> 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>>> 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>> > > > > 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 > > > > > > 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> > > 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
