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. 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. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>> >>>> >>>> >>>> >> >> ----- 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
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