sorry, I misspoke, the p-value will be different (perhaps very
different) between LI and --paired-diff. The p-value should not change
between LI and --paired-diff-norm; these two maps differ only by a scale
which is removed in the t-ratio.
doug
On 04/02/2013 01:15 PM, Yizhou Ma wrote:
> > If I do use the LI maps to perform my stats, which would be the
> > difference in interpretation between the results of using the
> > --paired-diff maps, and the standarized LI maps?
> The p-value will not change since the LI is just a scaled version of the
> paired-diff
> doug
>
>
> In my opinion, the interpretation will be different, and the
> difference just depends on the difference between (lh-rh) and LI
> themselves. The former tells you if the lh is bigger than the rh in
> absolute values, while the latter tells you to what extent it is
> asymmetrical. The latter is not a scaled, but a standarized version of
> the former. Which you use in your study really depends on which you
> are interested in conceptually.
>
>
> On Tue, Apr 2, 2013 at 12:30 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu <greve@nmr.mgh.harvard.edu>>> wrote:
>
> I think it is best to do it before the smoothing, though my
> results did
> not really change when I did it after.
> doug
>
>
> On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote:
> > sorry I meant to do the division, to standarize the LI after the
> > smoothing.
> >
> > El 02/04/13, *Gabriel Gonzalez Escamilla * <ggonesc@upo.es
> <mailto:ggonesc@upo.es <ggonesc@upo.es>>> escribió:
> >> Dear Doug,
> >>
> >> Interesting but, if I'm understanding this well, to get a
> normal LI,
> >> the --paired-diff-norm should be divided by 2 not multiplied,
> isn't it?
> >>
> >> standardLI = (lh-rh)/(lh+rh)
> >> FS_LI = (lh-rh)/((lh+rh)/2) <-- as you are dividing the
> denominator,
> >> your LI will be twice an standard one.
> >>
> >> Further, this division should be done before the smoothing, right?
> >>
> >> If I do use the LI maps to perform my stats, which would be the
> >> difference in interpretation between the results of using the
> >> --paired-diff maps, and the standarized LI maps?
> >>
> >> Regards,
> >> Gabriel.
> >>
> >>
> >> El 29/03/13, *Douglas N Greve * <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu <greve@nmr.mgh.harvard.edu>>> escribió:
> >>> The --xhemi flag causes both the left and right hemispheres of
> each
> >>> subject to be stacked into the output file. So the output file
> will
> >>> have
> >>> number of subjects x2 frames. The order is subject1.lh,
> subject1.rh,
> >>> subject2.lh, subject2.rh, ...
> >>>
> >>> If you add the --paired-diff, then you will get number of frames =
> >>> number of subjects, and each frame will be subject1.lh-rh,
> >>> subject2.lh-rh, etc
> >>>
> >>> If you use the --paired-diff-norm instead, then you will get
> what you
> >>> want subject1.(lh-rh)/((lh+rh)/2),
> subject2.(lh-rh)/((lh+rh)/2), etc.
> >>>
> >>> Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you
> >>> would
> >>> need to multiply the paired-diff-norm by 2.
> >>>
> >>> Finally, I want to point out that it may be better to smooth
> before
> >>> computing the LI because the LI computation is non-linear and
> it has
> >>> the
> >>> potential to divide by a noisy number. To do this, run without the
> >>> --paired-diff flags, then smooth, then run
> >>>
> >>> mri_concat yourfile.smoothed.mgh --paired-diff-norm --o
> >>> yourfile.smoothed.LI.mgh
> >>>
> >>> In my study, I ran it both ways and it did not make a
> difference, but I
> >>> think smoothing before LI is the safer bet.
> >>>
> >>> doug
> >>>
> >>>
> >>> On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote:
> >>> > Hi freesurfer experts,
> >>> >
> >>> > I'm investigating lh-to-rh asymmetry and am following
> instructions on
> >>> > this page :
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi.> >>> > My question is, what does the "--xhemi" flag do in the
> "mris_preproc"
> >>> > command? It seems to me that it calculates (lh-rh) value at each
> >>> > vertex for every subject. (I tried to use the same subject
> for each
> >>> > pair of input for "--paired-diff", and the result is not a
> all-zero
> >>> > output.)
> >>> >
> >>> > It would also be nice if someone can tell me how to realize
> my final
> >>> > goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each
> vertex
> >>> for
> >>> > each subject in a .mgh file.
> >>> >
> >>> > Thanks,
> >>> > Cherry
> >>> >
> >>> >
> >>> > _______________________________________________
> >>> > Freesurfer mailing list
> >>> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu <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 <greve@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
> <
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> >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> >>> Outgoing:
>
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> >>>
> >>> 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
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> >>>
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> >>
> >> --
> >> --------------------------
> >> PhD. student Gabriel González-Escamilla
> >> Laboratory of Functional Neuroscience
> >> Department of Physiology, Anatomy, and Cell Biology
> >> University Pablo de Olavide
> >> Ctra. de Utrera, Km.1
> >> 41013 - Seville
> >> - Spain -
> >>
> >> Email: ggonesc@upo.es <mailto:ggonesc@upo.es <ggonesc@upo.es>>
> >>
http://www.upo.es/neuroaging/es/> >
> > --
> > --------------------------
> > PhD. student Gabriel González-Escamilla
> > Laboratory of Functional Neuroscience
> > Department of Physiology, Anatomy, and Cell Biology
> > University Pablo de Olavide
> > Ctra. de Utrera, Km.1
> > 41013 - Seville
> > - Spain -
> >
> > Email: ggonesc@upo.es <mailto:ggonesc@upo.es <ggonesc@upo.es>>
> >
http://www.upo.es/neuroaging/es/>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu <greve@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing:
>
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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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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