I've written a script that will come out with version 6, but I've put it here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get info on how to run it. On 10/28/2016 05:10 PM, Daya P wrote: > Hi Doug, > > I needed to make a registration template and an cortical atlas because > I am trying to measure cortical thickness, GM and surface area on cat > brains. > > What would be the necessary changes? > Would it be possible (and appropriate) to use just > mris_left_right_register instead? > > Daiana > > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > A difference of 10 out of 500 or 1000 does not both me at all. Why > do you need to create your own atlas? It is doable for the cross > hemi stuff, it is just difficult. > > > On 10/26/16 10:16 AM, Daya P wrote: >> >> Thank you for your help! >> >> I created a registration template and atlas from scratch could I >> input that in the interhemispheric registration analysis? >> >> The ROIs for the diffrerent regions per hemisphere are 50-100 >> vertices >> >> On Oct 24, 2016 5:03 PM, "Douglas N Greve" >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> It would depend on how big the ROI is to begin with. Do you >> know that we >> have our own interhemispheric analysis that might be better >> for this? >> Check out >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi >> <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> >> >> >> On 10/24/2016 12:33 PM, Daya P wrote: >> > Hi Bruce, >> > >> > I drew ROIs on an initial subject and then after >> registering all other >> > subjects to the initial one, used mri_label2label to map >> the ROIs from >> > the initial subject to subsequent ones. >> > I am interested in looking at asymmetry between left and >> right regions. >> > >> > I had two concerns, one that the ROIs have different # >> vertices on >> > different subjects, but as you mentioned the nonlinear >> process makes >> > sense, since each subject does not have the exact same >> brain size and >> > curvature. >> > >> > Another concern was that the ROIs on the left and right >> hemisphere in >> > a subject do not have the exact same number of vertices. >> Would a >> > difference of 10 vertices max bias results? >> > >> > Thank you for your help, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl >> > <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@nmr.mgh.harvard.edu> >> <mailto:fis...@nmr.mgh.harvard.edu >> <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: >> > >> > Hi Daiana >> > >> > yes, that is to be expected given the nonlinear nature >> of the >> > cross-subject registration. It shouldn't bias things, >> although >> > you'll need to give us more details if you want a more >> definitive >> > answer. >> > >> > cheers >> > Bruce >> > >> > >> > >> > On Mon, 24 Oct 2016, Daya P wrote: >> > >> > Hi All, >> > >> > My question is about using mri_label2label. When >> mapping the >> > labels from one >> > subject to another the number of vertices of each >> ROI is >> > different. Is that >> > something to be expected? >> > >> > How much of a difference does a number of vertices >> of 50 >> > compare to 40 have >> > on measures like thickness, grey matter and surface >> area? >> > >> > I would really appreciate some help >> > >> > Thank you, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > >> > >> > _______________________________________________ >> > 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 >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> <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> >> > <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. >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto: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> >> 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 >> <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/ >> <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 >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > _______________________________________________ > 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
