Hi, Michael
Thanks for the guidance. Still I am unclear of how to implement your ideas
1 For the mris_anatomical_stats, should I use -a subjid/label/lh.aparc.annot or use the �Ct option to check the thickness file (what��s the name of this file)? If I understand it correctly, I will get a measure of ��average cortical thickness�� of each hemisphere for every subject and further I can set this as a control variable for regional thickness comparison?
2 for each of the cortical regions, there is also a volumetric measure. What average or overall volume measure I can use as a control variable, the ICV or something new from autorecon3?
Thanks
Karl
From: mharms@conte.wustl.edu To: rememberer@hotmail.com Date: Thu, 16 Dec 2010 12:04:35 -0600 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to adjust cortical thickness/area/volume measures from autorecon3
BTW: You can't "sum" the thicknesses across the various regions in the aparc files, as that would be a meaningless measure. You either need to compute the average cortical thickness as I suggested, or compute a weighted mean from the data in the aparc files, in which you weight each region's thickness by its proportion of the total surface area.
cheers, -MH
On Thu, 2010-12-16 at 11:57 -0600, Michael Harms wrote:
Yes, I think that using average cortical thickness is a reasonable covariate to use in thickness analyses. And total cortical surface area likewise if you are analyzing regional surface areas, although in the case of surface area you need to decide whether to use areas based on the GM or WM surface, or some "mid"-surface in-between.
Use mris_anatomical_stats along with the {lh,rh}.cortex.label files to compute these statistics for the overall cortex. If the optional <surface name> at the end of the command is 'pial', then the area will be based on the pial surface. If nothing is specified, it'll be based on the white (default) surface. If you want the area based on the mid- surface, you either need to construct that surface first (if it isn't already computed by recon-all in the most recent FS versions) or run the command separately for the 'pial' and 'white' surfaces and then average the resulting areas].
cheers, -MH
On Fri, 2010-12-17 at 01:42 +0800, Liukarl wrote:
Hello, Freesurfer experts:
I found to report subcortical volumetric measure, ie, the volume of amygdale, people tend to use icv as a control variable. Is there any corresponding measure to correct the cortical thickness/area/volume results from autorecon3. Because we have priori hypothesis of hemisphere dichotomy of cortical structures, we need some control variable for each hemisphere. We want to use an overall measure for each hemisphere as a control variable. For example, to measure the group differences on rh_paracentral_thickness, we will use the rh_whole_thickness as a contral variable (which is the sum of the thickness measures of all the ROIs in the right hemisphere produced by Freesurfer). Similarly, to measure the group differences on rh_paracentral_area and rh_paracentral_volume, we will use the rh_whole_area and rh_whole_area as a contral variable respectively. Is this a valid approach to report our results?
Thanks a lot!
Karl
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