Hi Bruce,
Thanks again for your help so far. I had a few follow up questions:
1) As far as mapping the average thickness to fsaverage coords, when I was constructing the average thickness map I used mris_preproc with --target fsaverage (and then mri_concat), so it's already in fsaverage coordinates right? Or do I need to apply mri_surf2surf?
2) I used read_curv to load it into matlab which gives a <n*1> matrix where I'm assuming that n is the number of total vertices of the cortex, right?
3) Concerning the binning in matlab, I know how to do it in the order of increasing vertex number, but I had trouble incorporating the [xyz] fsaverage coordinates. Is there a way to rearrange the matrix (that is the result of read_curv) into another matrix where the thickness values are sorted based on the fsaverage coordinates?
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, pfotiad@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, 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 >> >> >> > > _______________________________________________ > 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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