Thanks again, for the record, I'm using freesurfer version 5.3.0 on Centos 6. On 9/09/2014 11:00 PM, <_andre...@sapo.pt> wrote:
> 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 <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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