Thanks, Doug. This is very helpful!
On Fri, Mar 29, 2013 at 12:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
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 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 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.