Hi Doug, just a quick follow-up on my previous questions regarding custom average surfaces. I guess I am a bit confused regarding the relationship of custom templates and custom average surfaces. I made a custom template and a custom average surface. However, I don't understand how they are related to each other. Furthermore, I am wondering which is used when I use rawfunc2surface-sess. Thanks, Caspar
2013/8/19 Douglas Greve <gr...@nmr.mgh.harvard.edu> > > You can just copy in the T1.mgz from fsaverage (won't matter that it is > human), or you can try running make_average_volume to make a NHP volume. > Not sure that will work, but make sure to use --no-aseg > > doug > > > > On 8/19/13 8:43 PM, Caspar M. Schwiedrzik wrote: > > Hi Doug, > I ran make_average_surface.no-aparc and identity matrices on my data, and > I seems to have completed the averaging without an error. However, when I > try to view the result with tksurfer, I get an error because there is no > average T1 for the average subject. How would you recommend I go about > this? Do you have a make_average_volume.no-aparc as well, shall I make an > average T1 manually, or can I skip the average T1? > Thanks! > Caspar > > > > 2013/8/19 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > >> >> 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/ >> >> > >
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