Hi Panos no, mris_anatomical_stats won't do it. I would map the average thickness to fsaverage coords, then load that into matlab and go from there using the [xyz] coords of fsaverage for the binning, which is pretty much MNI305
cheers Bruce On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi Bruce, > > Sorry, I had a last follow up question. I just realized that the resulting > bins will be in the fsaverage space, and hence I wouldn't be able to use > mris_anatomical_stats to calculate the average thickness of the bins, > since the fsaverage "subject" does not have a wm.mgz file. Did you have > another way in mind to calculate the thickness of each bin, or do you > believe that mris_anatomical stats should do the trick with a specific > flag? > > Thanks a ton, > Panos > >> Hi Bruce, >> >> I see, that's really helpful, thank you! >> >> Best, >> Panos >> >> >>> Hi Panos >>> >>> I would make an average thickness map in fsaverage space, then in matlab >>> divvy up the a-p direction into bins (say 100 of them) and compute the >>> average in each bin based on the a/p coordinate >>> >>> cheers >>> Bruce >>> On Tue, 13 May 2014, >>> pfot...@nmr.mgh.harvard.edu wrote: >>> >>>> Hi Bruce, >>>> >>>> Just to clarify, when you say "average the thickness along each A/P >>>> coordinate" do you mean by looking up at the average cortical thickness >>>> of >>>> each parcellation and then calculating their average from P->A, or is >>>> there another way to find the average thickness of each slice and then >>>> see >>>> how that average changes from P->A? >>>> Thanks again for your time, >>>> Panos >>>> >>>>> I see. Then measure the thickness normally, then see how it changes in >>>>> those directions. You could average the thickness along each A/P >>>>> coordinate >>>>> - that wouldn't be a problem. You just don't want to measure it that >>>>> way >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Mon, 12 May 2014, >>>>> pfot...@nmr.mgh.harvard.edu wrote: >>>>> >>>>>> Hi Bruce, >>>>>> >>>>>> Thank you for your reply. I was interested in looking how the >>>>>> thickness >>>>>> changes from the posterior to the anterior side of the brain and vice >>>>>> versa (the thickness gradient). >>>>>> >>>>>> Thank you again for your time! >>>>>> Panos >>>>>> >>>>>> >>>>>>> Hi Panos >>>>>>> >>>>>>> it would certainly be possible to make that measurement, but it >>>>>>> wouldn't >>>>>>> tell you anything biologically interesting. Why would you want to do >>>>>>> such >>>>>>> a >>>>>>> thing? It will reflect the (arbitrary) image slice orientation and >>>>>>> not >>>>>>> the >>>>>>> brain. >>>>>>> >>>>>>> cheers >>>>>>> Bruce >>>>>>> >>>>>>> >>>>>>> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote: >>>>>>> >>>>>>>> Hi FS experts, >>>>>>>> >>>>>>>> I was wondering whether it would be possible to measure the average >>>>>>>> cortical thickness at a specific slice (either axial, coronal, or >>>>>>>> sagittal). I read in Bruce's paper: "Measuring the thickness of the >>>>>>>> human >>>>>>>> cerebral cortex from magnetic resonance images" that "Measuring the >>>>>>>> thickness from the coronal slice at the point indicated by the >>>>>>>> green >>>>>>>> cross >>>>>>>> would result in an estimate in excess of 1 cm." Is that always the >>>>>>>> case, >>>>>>>> or has there been a way to bypass that issue? >>>>>>>> >>>>>>>> Thank you for your time, >>>>>>>> Panos >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >> >> _______________________________________________ >> 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 > > > _______________________________________________ Freesurfer mailing list 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. 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