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We are trying to calculate the volume of grey matter of the significant clusters within each region identified by our initial analyses. Is there a procedure already written in matlab to accomplish this calculation?
Right now we've calculated the mean thickness across all subjects for each vertex, and then averaged those thickness across each region (or across each significant portion of a region). Then took the areas from the regions (calculated through Freesurfer’s mri_surfcluster program, which for the whole regions will obviously only get a single cluster, and total area of that cluster) and multiplied them by the mean thicknesses to get total area. It should be possible to do the same thing to get the significant volumes.
Does the above procedure seem like the most straightforward? Or does freesurfer have a program to do this more efficiently?
On 9/13/2021 10:11 PM, Brigitte Pace wrote:
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We are trying to calculate the volume of grey matter of the significant clusters within each region identified by our initial analyses. Is there a procedure already written in matlab to accomplish this calculation?
Right now we've calculated the mean thickness across all subjects for each vertex, and then averaged those thickness across each region (or across each significant portion of a region). Then took the areas from the regions (calculated through Freesurfer’s mri_surfcluster program, which for the whole regions will obviously only get a single cluster, and total area of that cluster) and multiplied them by the mean thicknesses to get total area.
This sounds something like a volume calculation
It should be possible to do the same thing to get the significant volumes.
Does the above procedure seem like the most straightforward? Or does freesurfer have a program to do this more efficiently?
If you want area and volume, you should run mris_preproc the way you did with thickness but use --meas area and --meas volume You can then run something like mri_segstats --i your.area.mgz --i ocn.mgz --ctab ocn.ctab --excludeid 0 --avgwf area.avgwf.dat area.avgwf.dat will be a table with rows being subject and column being cluster, ocn is the ocn from the cluster analysis you can repeat for volume
-- Brigitte Pace, M.A. Doctoral Student Clinical Psychology, Health Emphasis Ferkauf Graduate School of Psychology Yeshiva University Albert Einstein College of Medicine
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Brigitte Pace -
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