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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