Ah ok! Sorry... In both places?
Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: > It's .thresh.label, not .threshold.label. > > On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: > >> >> Hi Anastasia! >> >> The command in the recon-all.log is this one: >> >> mri_label2label --srcsubject fsaverage --srclabel >> /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label >> --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh >> --regmethod surface >> >> And I tried substituing BAxxx.label by BAxxx.thresh.label like this: >> >> mri_label2label --srcsubject fsaverage --srclabel >> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label >> --trgsubject SUSANAFERREIRA --trglabel >> ./lh.BA1.thresolh.label --hemi lh --regmethod surface >> >> gave an error : >> >> SUBJECTS_DIR /home/user/visao/Freesurfer/ >> FREESURFER_HOME /usr/local/freesurfer >> Loading source label. >> No such file or directory >> mri_label2label: could not open label file >> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label >> Illegal seek >> ERROR reading >> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label >> >> Thus, I substitued only in the second BAxxx.label and it worked. I >> thought that was it, but then the values >> were the same. I'm sorry, I'm not sure what is missing. >> >> Thank you! >> >> Andreia >> >> >> >> >> >> >> >> >> >> >> Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: >> >>> 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. 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