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>> 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. > 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: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> > 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> > 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. > > -- 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
