Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new files aren't being used in 5.0.
You'll need to find the "BA labels" section in recon-all.log and rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: > Hello list! > > Any suggestions on what I may be doing wrong? > > Thanks! > Andreia > > > > ----- Mensagem encaminhada de _andre...@sapo.pt ----- > Data: Sun, 24 Mar 2013 19:11:13 +0000 > De: _andre...@sapo.pt > Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume > Para: Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>, freesurfer > <freesurfer@nmr.mgh.harvard.edu> > Cc: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > > 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. 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 . 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