Re: [Freesurfer] mris_preproc with --xhemi

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> 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>> 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>> 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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>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
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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>
>> 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>
> 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>
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>
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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
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