Ok. So the first is the input and the second is the output, correct? So I'll have a different file for each out put? Is it possible to have a table with the different measures after the threshold?
Thank you very much and I apologize for the naive questions... Andreia Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: > What you call the output label is up to you. What you call the input > label is more important - it has to be a file that actually exists. > > On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: > >> 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 > > > > > > > > > > > > > > > > > > >>>> > > > > > > > > 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 > > > >>>> > > > > > > > > > > > > was > > > > > > > > > > > > > > > > > >>>> > > > > > > > > > >>>>>>>>>>>>>>>>>> >>>>>> >>>> > > > > > > > Bruce that I had > > > > > > > > > > > > > > > > > >>>> > > > > > > > > > > > > > >>>> > > > > > > > > > > > > > > > to >>>> > > > > > > > > > > > > > > > threshold the BA in order to have an >>>> > > > > > > > approximate > > > > > > > > > > area > > > > > >>>> > > > > > > > > > > > approximate > > > > > > > > > > when >>>> > > > > > > > > > > > > > > >>>>>>>>>>>>> overlaying >>>> > > > > > > > > > > > > > > > in the inflated surface. To >>>> get > > > > > > > > > > > > > > > > surface area >>>> > > > > > > > values > > > > > > > > > > I > > > > > > > > >>>> also > > > > > > > > > values > > > > > > > > > > > > > >>>> > > > > > > > > > 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 > > > > >>>> > > > > > > > > > > > > table > > > > > > > > > > > > > > > > > >>>> > > > > > > > > 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 > > > > > > > > for > > > > > > > > > > > > > > > >>>> > > > > > > > > > > > >>>>>>>>>>>>> analysis >>>> > > > > > > > > > > > > > > > since there are the thresolds issue. >>>> > > > > > > > > > > > > > > > > > > > I want to study mainly >>>> > > > > > > > > > > > > > > > > > > > > cortical >>>> > > > > > > > thickness > > > > > > > > > > > > > > and > > >>>> > > > > > > > > > > > > thickness > > > > > > > > > > > > > > > > > >>>> > > > > > > > > > > surface > > > > > > > > > > > > > > > > >>>> > > > > > > > > > > > > > > > > > >>>> > > > > > > > > > area but > > > > > > > > > > > > > > > > > > >>>> > > > > > > > > > > > > > > > >>>> > > > > > > > > > > > > > > also >>>> > > > > > > > > > > > > > > > look also at the volume (which is >>>> > > > > > > > surface-based, > > > > > > > > > > thus >>>> > > > > > > > > > > > > > > > thickness*surface are will not >>>> be = > > > > > > > > > > > > > > > > volume >>>> > > > > > > > since > > > > > > > > > > they > > > > > > > >>>> > are > > > > > > > > since > > > > > > > > > > an > > >>>> > > > > > > > > > > > >>>>>>>>>>>>> > average >>>> > > > > > > > > > > > > > > > from each label, right?). >>>> > > > > > > > > > > > > > > > > > > > I' not sure of which >>>> approach > > > > > > > > > > > > > > > > > > > > to >>>> > > > > > > > follow > > > > > > > > > > > > > > now... > > >>>> > > > > > > > > > > > > follow > > > > > > > > > > > > > > > > > >>>> > > > > > > > > > > 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 . > > > > > > > > > > > > >>>> > > > If >>>> > > > > > > > the > > > > > > > > > e-mail was > > > > > > >>>> > sent > > > > > > > > the > > > > > > > > > > > > >>>> > > > > > > > > > to > > > > > > > > > > > > you in error >>>> > > > > > > > > > > > > > > but does not contain patient > > >>>> > > > > > > > > > > > > > information, >>>> > > > > > > > please > > > > > > > > > contact > > > > > > >>>> > the > > > > > > > > please > > > > > > > > > > > > >>>> > > > > > > > > > sender > > > > > > > > > > > > and properly >>>> > > > > > > > > > > > > > > dispose of the e-mail. >>>> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > > > > > > > > > > > > > > > ----- Fim de mensagem >>>> reenviada ----- >>>> > > > > > _______________________________________________ >>>> > > 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 >>>> > > >> >> >> >> >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
