I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run
tkregister2 --fstal --s subject It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity doug On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > that's great, thank you very much. > From the previous posts I assume that this does not solve the issue > with the missing Talairach.xfm. Do you have a recommendation for that? > Thanks, Caspar > > > 2013/8/19 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > > I've put that script here > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc > > > On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: > > Hi Freesurfer experts, > > I am trying to make an average surface from several monkey surfaces, > > and I ran into a problem with make_average_subject. > Specifically, I do > > not have an aparc file nor a talairach.xfm. It seems that these > > problems have come up on the list before > > > > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). > > I tried to download make_average_surface.no-aparc, however, the link > > seems to be broken. Also, I couldn't find a solution to the missing > > talairach.xfm on the list. > > It would be great if you could provide me with a working link to > > make_average_surface.no-aparc; any suggestions regarding making an > > average surface without talairach.xfm would be appreciated. > > I already made a new template and aligned all individual surfaces to > > this template. > > > > Thanks! > > Caspar > > > > > > > > _______________________________________________ > > 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. > > -- 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
