Hi Bruce and Doug, thank you both so much for your help. >> You could generate it yourself easily enough >> though. For now I am taking the geometric average between pial and white surface coordinates. Is that the right way to do it, or is there a more precise way?
Also: If I decided to represent the stuff on the mid-surface, would it then also make sense to also take the average of pial.avg.area.mgh white.avg.area.mgh as the area estimation at each vertex? Many thanks, Boris On 2011-05-12, at 4:08 PM, Douglas Greve wrote: > Yes, the avg.area files have the average over the input subjects at each > vertex. I've used it to overcome this problem. > doug > > On 5/12/11 8:04 AM, Bruce Fischl wrote: >> 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 >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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