I don't think this makes sense unless you have created a new label atlas for your individual subjects. The current label atlas exists in the fsaverage space. Maybe Bruce can weigh in.
On 03/05/2015 04:46 PM, Jason Tourville wrote: > Hi Doug, > Perhaps I should back up and explain our goal. We are using Freesurfer > to recon pediatric data sets and are planning to use the surface > labels as seeds for connectivity studies and for morphometric > analyses. We're concerned that using the fsaverage surface template as > the target for surface registration could introduce errors in the > labels due to match with our pediatric surfaces, so we derived a new > surface template from a subset of our data set. > > My understanding is that once we've done this, to get the surface > labels, stats, etc. for each scan, we need to then register each scan > to this new target and then run the the various steps to get the > labeled surfaces (e.g., mris_ca_label). So I want to confirm this; > more specifically, I'd like to know which steps of the recon-all > pipeline need to be rerun to to replace completely replace the > fsaverage target. > > Jason > > > On Thu, Mar 5, 2015 at 3:58 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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> > <mailto: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> > <tel:%28617%29353-9484> > > >> Fax: (617)353-7755 <tel:%28617%29353-7755> > <tel:%28617%29353-7755> > > >> > > >> > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel: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> > > 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> > > <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> > <mailto: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 <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 > > > > > -- > 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
