great thanks Doug!
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 greve@nmr.mgh.harvard.eduwrote:
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.kelly16@gmail.com mailto:krista.kelly16@gmail.com> wrote:
Great Thanks! On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 contactthe
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