correct, unfortunately, the "White" label is hard coded into the program.
On 09/14/2014 02:24 AM, will brown wrote: > Thanks Doug, > > Just to double check I understand you correctly, where the output says > "# Measure Cortex, WhiteSurfArea, White Surface Total Area" this is > now the surface area of the pial surface even though it is labeled White? > > Cheers, > Will > > On Sat, Sep 13, 2014 at 3:27 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > 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> > <mailto: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> <mailto: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> > <mailto: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> > <mailto: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> > <mailto: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> > <mailto: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> > <mailto: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> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- 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
