You can run something like cd $SUBJECTS_DIR/subject
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 subject lh pial The "Measure Cortex" fields in the output stats/lh.aparc.pial.stats will be measures of the pial surface as will the SurfArea, MeanCurv, GausCurv, FoldInd, and CurvInd fields for each ROI (thickness and number of vertices will stay the same) doug On 09/11/2014 07:29 PM, will brown wrote: > 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 <mailto: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 <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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 <mailto: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 > <mailto: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 <mailto: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. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
