Hi Will, Just to clarify, what version of FS are you using? I think it might not be 5.0 and I don't know if everything aplies if we are using different versions.
1) Yes, it is only based on the pial surface (and these command lines are for the aparc, DK altas). The second set provides the surface area for each hemisphere without including, for example, the pial surface that you see in the hippocampus which is not accurate and one should not care about. In the end, the second set gives you the sum of the areas in aparc, thus, you can just make a sum of that parcellation if you want. I just realized that. 2) No. In the new stats file, the value that you want is at the bottom: # ColHeaders StructName NumVert SURFAREA GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd And when running aparcstats2table that's the value you should get in the table. I think that # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA may be including more stuff since it is bigger. If what you want is only the total hemisphere surface area you only need to run the second set of commands. If you want the area of each DK altas parcellation then run the first set and then simply add them to get total hemisphere surface area. Someone from Freesurfer staff will correct me if I'm wrong. (Please) I'm Ccing Doug since he was replying to your previous emails. Let's wait for their feedback. Andreia Citando will brown <willbrown1...@gmail.com>:
Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things; 1) The first commands you have given provide the stats for the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex? 2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA, ? Thanks again, Will On Tue, Sep 9, 2014 at 5:36 PM, will brown <willbrown1...@gmail.com> wrote:Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary. Will On Wed, Sep 3, 2014 at 1:12 AM, <_andre...@sapo.pt> wrote:_Hi Will, I use the following commands to get surface area from the pial surface: In the subject label dir:_ _mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.APARC.PIAL.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial_ _mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.APARC.PIAL.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial _ _Then run aparcstats2table using APARC.PIAL instead of aparc (only because I called this new parcellation aparc.pial) To get the total surface area of each hemisphere I use: In the subject stats dir:_ _mris_anatomical_stats -l ../label/lh.cortex.label -f lh.TOTAL_PIAL.stats -b SUBJ lh pial_ _mris_anatomical_stats -l ../label/rh.cortex.label -f rh.TOTAL_PIAL.stats -b SUBJ rh pial_ _Then run aparcstats2table using TOTAL_PIAL instead of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like)_ _Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir. I use FS 5.0. Is this what you want? Best, Andreia_ _Citando will brown <willbrown1...@gmail.com>:__Hi all, _ _ _ _I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info._ _ _ _?.aparc.stats reports:_ _ _ _Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2_ _ _ _How about the gray matter?_ _ _ _Thanks,_ _Will_ _ _ _ __ _
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