Hi Doug, As I'm trying to run mris_preproc on this page ( http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I want to know what the --xhemi argument is for. Is it for calculating the difference between lh and rh thickness?
I wanted to calculate a asymmetry index for each vertex, which is (lh-rh)/[(lh+rh)/2] rather than (lh-rh). Can I do that using mris_preproc and how? Thanks, Cherry On Thu, Mar 28, 2013 at 1:32 PM, Ejoe Yizhou Ma <ym...@nyu.edu> wrote: > I see. Then I think I'd better just follow the instructions on the Xhemi > page. Thanks! > > > On Thu, Mar 28, 2013 at 1:06 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Hi Cherry, what I meant was that you cannot use the qcache with xhemi. >> You'll need to run the mris_preproc command as listed on the web page. >> doug >> >> >> On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote: >> >>> Thanks, Doug. >>> >>> I'm not planning to use qdec. It's just that I used to generate the >>> ?h.thickness_max10.fwhm10.**fsaverage_510.mgh files (which are what we >>> name the files after running the two commands) before I use mris_preproc >>> and mri_glmfit. I also generally skip the "smooth" step in freesurfer >>> tutorial since the files are smoothed in the first place. >>> >>> Any suggestions? >>> >>> Cherry >>> >>> On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve < >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >>> wrote: >>> >>> >>> >>> Actually, #2 will not work. I don't think you can use qdec with the >>> xhemi stuff anyway. You should use the mris_preproc command >>> followed by >>> mri_glmfit. >>> doug >>> >>> >>> On 03/28/2013 12:51 PM, Douglas N Greve wrote: >>> > On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: >>> >> Dear Freesurfer experts, >>> >> >>> >> I'm trying to investigate lh-to-rh asymmetry, so I register my >>> >> subjects to the subject of fsaverage_sym following the >>> instructions on >>> >> this page: >>> http://surfer.nmr.mgh.harvard.**edu/fswiki/Xhemi<http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> >>> . >>> After all >>> >> the surfreg commands I've got ?h.thickness files in >>> subjid/xhemi/surf. >>> >> >>> >> In my lab we generally process ?h.thickness files with the next >>> two >>> >> commands before statistically analysis: >>> >> >>> >> "mris_thickness -max 10 subjid ?h thickness_max10" >>> >> "recon-all -qcache -measure thickness_max10 -target fsaverage_510 >>> >> -fwhm 10 -no-isrunning -s subjid -hemi ?h" >>> >> >>> >> To keep with this protocol, my questions are >>> >> 1) how do I use "mris_thickness" properly so that I don't >>> overwrite >>> >> the files registered to fsaverage_510? >>> > I think it will recreate the basic ?h.thickness file and will >>> not touch >>> > registrations. >>> >> 2) in "recon-all -qcache", will it do the trick by substituting >>> >> "fsaverage_sym" for "fsaverage_510"? >>> >> >>> > Yes, that should work. >>> >> Thank you in advance, >>> >> Cherry >>> >> >>> >> >>> >> >>> >> ______________________________**_________________ >>> >> Freesurfer mailing list >>> >> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >>> > >>> >>> >> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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> >>> >>> <http://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> >>> >>> <http://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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >>> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >>> >>> >>> >> -- >> 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<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >
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