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> 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> 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 >>> > 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 >>> >>> >>> 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 >> 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 > 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
