On Mon, Jan 13, 2014 at 6:25 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

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

> <greve@nmr.mgh.harvard.edu <mailto:greve@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.kelly16@gmail.com <mailto:krista.kelly16@gmail.com>

> > <mailto: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>

> <mailto: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>>
> > <mailto: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
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
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> > > >
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> > >
> > > --
> > > 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>>
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> <mailto:greve@nmr.mgh.harvard.edu>>>
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> > --
> > 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>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
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--
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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