Sure. We'd like to know how to find the surface area of the cortical grey matter from the pial surface. So specifically, what is the surface area of the pial/grey matter boundary of the cortex for each hemisphere?
We're using Freesurfer v5.3 on Centos 6. Thanks, Will Brown On Fri, Sep 12, 2014 at 9:11 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > sorry, this thread has gotten too deep. Can someone summarize the question? > > > On Thu, 11 Sep 2014, _andre...@sapo.pt wrote: > > >> Ok. Then, I'm not sure if everything is correct with the command lines >> since >> I use 5.0. >> >> Any thought on this Freesurfer team? >> >> Thanks, >> Andreia >> >> Citando will brown <willbrown1...@gmail.com>: >> >> 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>: >> >> 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 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. 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