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