Hi Bruce, I was having issues with the part after that, that is how to calculate the average thickness of those bins, after I create them. Thanks again Best, Panos
> 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 > > > _______________________________________________ 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. 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.
