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 * <gr...@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 >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu >> <gr...@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 * <ggon...@upo.es >> > <mailto:ggon...@upo.es <ggon...@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 * <gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu <gr...@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 >> > >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu >> <gr...@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: >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >>> >> > >>> _______________________________________________ >> > >>> 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 >> > >>> >> > >>> >> > >>> 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 >> > Compliance >> > >>> HelpLine at >> > >>> http://www.partners.org/complianceline . If the e-mail was >> sent to >> > >>> you in error >> > >>> but does not contain patient information, please contact the >> > sender >> > >>> and properly >> > >>> dispose of the e-mail. >> > >>> >> > >> >> > >> -- >> > >> -------------------------- >> > >> 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: ggon...@upo.es <mailto:ggon...@upo.es <ggon...@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: ggon...@upo.es <mailto:ggon...@upo.es <ggon...@upo.es>> >> > > http://www.upo.es/neuroaging/es/ >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu >> <gr...@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: >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> > _______________________________________________ >> > 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 >> gr...@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 >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > -------------------------- > 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: ggon...@upo.es > http://www.upo.es/neuroaging/es/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
