The mris_register command is what does the registration and creates a new sphere.reg file. surfreg just implements that command mris_register command.
I'm not sure what you mean by the labeling steps. On 03/05/2015 03:53 PM, Jason Tourville wrote: > Hi Doug, > I've run the steps outlined in the SurfaceRegAndTemplates page so far. So: > make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ... > > foreach subject (subj1 subj2 subj3 ...) > cd $SUBJECTS_DIR/subject > mris_register -curv surf/lh.sphere \ > $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \ > surf/lh.sphere.reg.newtemplate > end > > mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 > ... > > make_average_subject --out newnewtemplate --surf-reg > sphere.reg.newtemplate \ > --subjects subj1 subj2 subj3 ... > > My understanding is that the next step is to now register each > individual surface to this new template and then run through the > surface (and volume) labeling steps. Is that correct? > > It occurs to me that the fsaverage template used as the target for any > .gcs that I would to label the surface. Will I have to account for this? > > Thanks again, > Jason > > > > > On Thu, Mar 5, 2015 at 3:26 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > If you used make_average_subject to create the template, you can run > surfreg to do the registration. If/when you run mris_preproc, make > sure > to spec both the target subject and the new spherical registration > > > On 03/05/2015 03:18 PM, Bruce Fischl wrote: > > Hi Jason > > > > I don't think so - you'll probably have to edit the recon-all > script. And > > by template do you just mean the folding pattern .tif files, or > do you > > meant the parcellation atlases (*.gcs)? > > > > cheers > > Bruce > > On Thu, 5 Mar 2015, Jason Tourville > > wrote: > > > >> Greetings, > >> I have generated custom surface templates from pediatric data > sets. To apply > >> it to the larger data set, is it sufficient to simply run the > autorecon3 > >> steps (perhaps skipping the mris_sphere step)? If so, is there > a handy flag > >> for running this with recon-all and/or a way to run autorecon3 > with a flag > >> indicating that the non-default template should be used? > >> > >> Once I've done this, I'd like to do some form of comparison b/w the > >> templates. I am considering looking at the overlap of surface > labels > >> generated by the custom templates to a manually labeled "gold > standard." > >> Does that sound reasonable? Do you have any other suggestions? > >> > >> Best, > >> Jason > >> > >> -- > >> Jason A. Tourville, Ph.D. > >> Research Assistant Professor > >> Department of Speech, Language, > >> and Hearing Sciences > >> Boston University > >> 677 Beacon St. > >> Boston, MA 02215 > >> Phone: (617)353-9484 <tel:%28617%29353-9484> > >> Fax: (617)353-7755 <tel:%28617%29353-7755> > >> > >> > > _______________________________________________ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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. > > > > > -- > Jason A. Tourville, Ph.D. > Research Assistant Professor > Department of Speech, Language, > and Hearing Sciences > Boston University > 677 Beacon St. > Boston, MA 02215 > Phone: (617)353-9484 > Fax: (617)353-7755 > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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
