Hi Paolo, Are you showing individual subject data in the MNI space, or group average data? In general showing template brains and average data is not a good idea. It misrepresents the spatial localization accuracy of the data. You should try to use averages of the anatomy for groups of tracts of average fmri data or other group stats/data.
cheers Bruce On Mon, 7 Nov 2011, Paolo wrote: > I think it is well possible. > And in principle i just wanted to use it for presentation, but the > fsaverage doesnt really look like a "template" brain, rather like an average > > that's why i was wondering whether there is a more realistic template > available in freesurfer space, or how i can create one > (the idea was to recon-all the MNI152, which to me resembles much more > to a brain) > > would it be the correct approach, or do you have other suggestions? > by the way is it normal that recon-all on mni152 takes just ages to > complete? (>12 hours on an athlon64, dont know exactly how long, i > always stopped it before it finished) > > Paolo > > > On 07-Nov-11 16:03, Thomas Yeo wrote: >> I am probably wrong, but doesn't the volumetric part of fsaverage >> correspond to MNI305 space rather than MNI152 space? >> >> --Thomas >> >> On Mon, Nov 7, 2011 at 9:00 AM, Bruce Fischl<[email protected]> >> wrote: >>> Hi Paolo, >>> >>> I think fsaverage has this in the aseg.mgz. >>> >>> cheers >>> Bruce >>> On Mon, 7 Nov 2011, Paolo wrote: >>> >>>> In the meanwhile i did some research, and it looks like freesurfer does >>>> not use MNI152 as default template, am i right? >>>> it seems that the default template is the fsaverage subject, which in >>>> fact does not look like very realistic. >>>> >>>> >>>> Is there any way to get a realistic brain& segmentation that is >>>> "idealized" enough, and still in talairach space (freesurfer space)? >>>> >>>> maybe the MNI152 after recon-all and mri_transform to apply back the >>>> transformation? >>>> >>>> i am sorry if these questions look unreasonable, i am new of freesurfer, >>>> and still have problem orienting myself in the documentation :) >>>> >>>> best, >>>> Paolo >>>> >>>> On 05-Nov-11 00:57, Paolo wrote: >>>>> Hello >>>>> >>>>> I am a new user of freesurfer. >>>>> I was wondering whether the brain regions for the MNI152 dataset are >>>>> available anywhere (i mean the template brain regions for the default >>>>> MNI152 template). >>>>> >>>>> >>>>> I have also another question: i have the dti fiber tracts extracted and >>>>> computed and already in .trk format. >>>>> I was wondering: to bring them back into the template MNI152 space, is >>>>> it sufficient to apply the talairach.xfm transformation matrix to the >>>>> vertex data, or do i also need to use the m3z files (which look like a >>>>> nonlinear deformation field)? >>>>> >>>>> thanks in advance! >>>>> Paolo >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> 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. >>> >>> > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
