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, pfotiad@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, pfotiad@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, pfotiad@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
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