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 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.
