Hi Boris, 1. Doug can say for sure, but I believe so. 2. No. The mid surface doesn't correspond to any boundary in the image and so we are always hesitant to provide any morphometric measures for it. We are working on a more explicit estimation of the location of layer IV, but that is a future direction. You could generate it yourself easily enough though.
cheers Bruce On Thu, 12 May 2011, Boris Bernhardt wrote: > Hi Bruce, > > Thanks a lot for your reply. > >> 2. The surface area of fsaverage is less than any individual, so you >> *definitely* don't want to use it. You should map the ROI back to >> individuals and compute it in the native space. > > I have two follow-up questions: > > > 1) Do .pial.avg.area.mgh and/or .white.avg.area.mgh then store the mean native space surface areas for the individuals that were used to create fsaverage, and can I use these values to approximate the surface area of my ROIs then? > > 2) Do the avg.area files also exists somewhere for the half-thickness > mid-surface? If not, does it make sense to approximate the mid-thickness > surface area at each vertex by taking the mean of the corresponding > pial.avg.area and white.avg.area entries? > > Many thanks, > Boris > > >> >> cheers >> Bruce >> >> >> On Wed, 11 May 2011, Boris Bernhardt wrote: >> >>> Hello Freesurfer-experts, >>> >>> I just analyzed some FreeSurfer cortical thickness data that have been >>> surface-resampled to fsaverage (using mris_surf2surf with -s fsaverage). >>> >>> For the visualization and reporting of my findings, I have a two questions: >>> >>> 1. Is there anything that conceptually speaks against showing my results on >>> non-inflated surfaces of fsaverage, such as the white matter surface, the >>> pial surface, or even a mid-surface model? >>> >>> 2. I have a couple of ROIs defined on the surface of fsaverage and want >> to report the surface area of a given ROI in mm^2. Should I calculate the >> area of a ROI directly from the given surface of fsaverage, or to take the >> area computations from ?h.pial.avg.area.mgh/?h.white.avg.area.mgh which >> represent the averages of the individuals that went into fsaverage. >>> >>> I am asking because I was slightly unclear of the wiki-instructions: >>> https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface >>> suggests to use ?h.pial.avg.area.mgh; >>> >>> on the other hand, the more recently edited >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAverage >>> says that "The surface area of the new average subject (fsaverage) is that >>> of a typical subject" >>> >>> I am using freesurfer 4.5.0. >>> >>> Hope my questions make sense and thank you very much for answering them, >>> Boris >>> >>> >>> >>> >>> --- >>> Boris Bernhardt, PhD >>> Max Planck Institute for Human Cognitive and Brain Sciences >>> Stephanstr. 1a, 04103 Leipzig, Germany >>> >>> p: +(49) 341 9940 2658 >>> e: bernha...@cbs.mpg.de >>> http://www.cbs.mpg.de/~bernhardt >>> >>> >> >> >> 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. >> > > --- > Boris Bernhardt > Max Planck Institute for Human Cognitive and Brain Sciences > Stephanstr. 1a, 04103 Leipzig, Germany > > p: +(49) 341 9940 2658 > e: bernha...@cbs.mpg.de > http://www.cbs.mpg.de/~bernhardt > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
