I don't know what you mean by "real". Is the LI not real? The LI will
remove the effect of scaling (eg, brain size).
On 04/02/2013 04:48 PM, Gabriel Gonzalez Escamilla wrote:
> So, this means that the real differences is as Yizhou wrote?
>
> One measures the asymmetry (measured as the difference between lh-rh),
> and the LI or --paired-diff-norm will tell the extent of this asymmetry.
>
> Regards,
> Gabriel.
>
>
> El 02/04/13, *Douglas N Greve * <greve@nmr.mgh.harvard.edu> escribió:
>>
>> 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>
>> <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> <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> <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
>> > >>> >
>> > >>> >
>> > >>> > _______________________________________________
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>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <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>
>> <greve@nmr.mgh.harvard.edu>>
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>> > >>> Fax: 617-726-7422 <tel:617-726-7422>
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>> > <
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>> > <
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> > >>> Outgoing:
>> >
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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> <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> <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>
>> <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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>> > <
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:
>> >
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> >
>> > _______________________________________________
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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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> --
> --------------------------
> 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
>
http://www.upo.es/neuroaging/es/ --
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
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