Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label.
So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: > Sounds like centos4 is probably the safest bet for you, although you > should ask the list this question. > > Sorry, I don't know what values you want to get in a table. > > On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: > >> Ah ok! Anyway, I'm thinking of working with 5.2, should I download >> the version for centOS 4 then? >> >> After running the new BAxxx.thresh.label files how can I get the >> values in a table? >> >> >> >> >> Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: >> >>> It doesn't matter. You just need to use those .label files from >>> the fsaverage directory in the 5.2 distritbution. You don't need >>> to run any of the executables from the 5.2 distribution. >>> >>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: >>> >>>> I'm using Centos5, which file should I download? The one for >>>> CentOS 6 or > 4? >>>> > > Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: >>>> > > You'll need to go to the section of recon-all.log under the >>>> heading "BA > > labels". You'll need to rerun the commands in >>>> that section, but instead > > of using the BAxxx.label files, us >>>> the BAxxx.thresh.label files, which > > you'll find in the >>>> fsaverage subject dir in the 5.2 distribution. >>>> > > > On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: >>>> > > > > Hello Anastasia, >>>> > > > How should I proceed to get the different BAs measures >>>> output with > > > > FS > 5.0? >>>> > > > Thank you very much! >>>> > > > Andreia >>>> > > > > Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: >>>> > > > > The thresholded labels are in the 5.2 version of >>>> fsaverage > > > > > under: >>>> > > > $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label >>>> > > > > > On Sat, 23 Mar 2013, Bruce Fischl wrote: >>>> > > > > > > Anastasia? >>>> > > > > On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: >>>> > > > > > > Ok, that was my guess... I am running against a >>>> deadline, > > > > > > > any > > > > > news on >>>> > > > > > automatically computing the correct threshold script? >>>> Will I > > > > > > be > > > > able to >>>> > > > > > use it in 5.0? >>>> > > > > > > > Thanks you! >>>> > > > > > > > Andreia >>>> > > > > > > > > > Quoting Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>> > > > > > > > > yes. Surface area will be the affected much >>>> more than > > > > > > > > > > > > > > > > thickness (and > > >>>> > > volume of > > > > > > > > > course scales with area) >>>> > > > > > > > On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: >>>> > > > > > > > > Hi Bruce, >>>> > > > > > > > > > Thank you for the quick response! >>>> > > > > > > > > > In the meanwhile, does that also apply to >>>> cortical > > > > > > > > > > > > > > > > > > thickness > > >>>> > > > > and > > > > > > > > > > > > volume? >>>> > > > > > > > > > Thank you! >>>> > > > > > > > > > Andreia >>>> > > > > > > > > > Quoting Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>> > > > > > > > > > > Hi Andreia >>>> > > > > > > > > > > > the issue is that the BA labels contain >>>> every > > > > > > > > > > > > point > > > > > > > > > > >>>> that > > > > > > > > > > > > > > > > > > > > has any > > > >>>> non-zero >>>> > > > > > > > > probability (no matter how small!) of being >>>> in that > > > > > > > > > label. > > > > > > > So > > > > >>>> > the > > > > > > > > > > > > total >>>> > > > > > > > > label area is almost certainly always bigger >>>> than the > > > > > > > > > > > > > > > > actual > > > > > >>>> BA. > > > > > > > > > > > > Anastasia >>>> > > > > > > > > has some scripts for automatically computing >>>> the > > > > > > > > > correct > > > > > > > > > > > > >>>> threshold, > > > > > > > > > > > > and I >>>> > > > > > > > > believe she and Nick integrated them into 5.2 >>>> so that > > > > > > > > > the > > > > > > > stats > > > > >>>> > are >>>> > > > > > > > > computed both thresholded and unthresholded, >>>> > > > > > > > > > hopefully > > > > > > > they can > > > > >>>> > > > > > > > > > > > > > comment. >>>> > > > > > > > > Bruce >>>> > > > > > > > > > > > > > > > > > On Fri, 22 Mar 2013, > > > >>>> > > > > > > > > > > > > > > > _andre...@sapo.pt >>>> > > > > > > > > wrote: >>>> > > > > > > > > > > > > Hi all, >>>> > > > > > > > > > > > > > I'm using FS 5.0 and some time ago >>>> I was > > > > > > > > > > > > > > told by > > > > > > > > > > >>>> > > > > > > > > > > > > > > > > > > > > > > > > > > >>>> Bruce that I had > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > > > to >>>> > > > > > > > > > threshold the BA in order to have an >>>> approximate > > > > > > > > > > area > > > > > > > > when >>>> > > > > > > > > > > > > > > > > > > > > overlaying >>>> > > > > > > > > > in the inflated surface. To get surface >>>> area values > > > > > > > > > > I > > > > > > > > also > > >>>> > > > > need to > > > > > > > > > > > > > > use >>>> > > > > > > > > > the label_area and put a threshold >>>> > > > > > > > > > having the possibility to choose the >>>> surface that I > > > > > > > > > > > > > > > > > > want, > >>>> > > > > > either > > > > > > > > > > > > > > white >>>> > > > > > > > > > or pial. >>>> > > > > > > > > > > > > > But I can also get the BA stats in >>>> a table > > > > > > > > > > > > > > for > > > > > > > > > > > >>>> > all > > > > > > > > > > > > > > > > > > > > > > > > >>>> subjects and > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > areas >>>> > > > > > > > > > using either mris_anatomical_stats (on each >>>> label) > > > > > > > > > > or > > > > > > > > usinga > > > >>>> > > > > > > > > > > > > > > > > > script by >>>> > > > > > > > > > Jamaan to get the table (since I already >>>> have the > > > > > > > > > > > > > > > > > > ?.BA.stats > >>>> > > > > > > > > > > > > > > > > > > > files), >>>> > > > > > > > > > right? >>>> > > > > > > > > > > > > > My question is, which is the >>>> better/correct > > > > > > > > > > > > > > way > > > > > > > >>>> > > > > > to > > > > > > > > > > > > > > > > > > > > > > > >>>> > get the > > > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > thickness >>>> > > > > > > > > > and surface area values of the BA to export >>>> for > > > > > > > > > > > > > > > > > > statistical > > > >>>> > > > > > > > > > > > > > > > > > analysis >>>> > > > > > > > > > since there are the thresolds issue. >>>> > > > > > > > > > > > > > I want to study mainly cortical >>>> thickness > > > > > > > > > > > > > > and > > > > > > > > > > >>>> > > surface > > > > > > > > > > > > > > > > > > > > > > > >>>> > area but > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > also >>>> > > > > > > > > > look also at the volume (which is >>>> surface-based, > > > > > > > > > > thus >>>> > > > > > > > > > thickness*surface are will not be = volume >>>> since > > > > > > > > > > they > > > > > > > > are an > > >>>> > > > > > > > > > > > > > > > > > > average >>>> > > > > > > > > > from each label, right?). >>>> > > > > > > > > > > > > > I' not sure of which approach to >>>> follow > > > > > > > > > > > > > > now... > > > > > > > > > > >>>> > > Does > > > > > > > > > > > > > > > > > > > > > > > > >>>> it depend on > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > the >>>> > > > > > > > > > measure I'll be using? >>>> > > > > > > > > > > > > > Thank you! >>>> > > > > > > > > > > > > > Andreia >>>> > > > > > > > > > > > > > > > > > >>>> _______________________________________________ >>>> > > > > > > > > > Freesurfer mailing list >>>> > > > > > > > > > Freesurfer@nmr.mgh.harvard.edu >>>> > > > > > > > > > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> > > > > > > > > > > > > > > > > > > > > >>>> _______________________________________________ >>>> > > > > > > > > Freesurfer mailing list >>>> > > > > > > > > Freesurfer@nmr.mgh.harvard.edu >>>> > > > > > > > > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> > > > > > > > > > > > > > > The information in this e-mail is >>>> > > > > > > > > > > > > > > > intended > > > > > > > > > > > >>>> > > > > > > > > > > > > > > > > > only for > > > > > > > > > >>>> > > the > > > > > > > > > > > > > > > person to > > > > > > >>>> > > > > > > > > > > > > > > > > > > > > > > > > > whom it >>>> is >>>> > > > > > > > > addressed. 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