If you replace *every* occurence of BAxxx.label with BAxxx.thresh.label, this will keep things simple and you won't have to worry about which one is input and which one is output.
Run *all* the commands from the "BA labels" section, all the way to the end of that section, this will get you to the stats.
On Mon, 25 Mar 2013, _andreia_@sapo.pt wrote:
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 ayendiki@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, _andreia_@sapo.pt wrote:
Ah ok! Sorry... In both places?
Quoting Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu:
It's .thresh.label, not .threshold.label.
On Mon, 25 Mar 2013, _andreia_@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 > > > > > > > > > ayendiki@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, _andreia_@sapo.pt wrote: > > > Hello list! > > > > Any suggestions on what I may be doing wrong? > > > > Thanks! > Andreia > > > > > > > > > > ----- Mensagem encaminhada de > > > > > > > > > > _andreia_@sapo.pt ----- > Data: Sun, 24 Mar 2013 19:11:13 +0000 > De: _andreia_@sapo.pt > Assunto: Re: [Freesurfer] Brodmann area thickness, surface area > and > > > volume > Para: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu, > > > > freesurfer > freesurfer@nmr.mgh.harvard.edu > Cc: Bruce Fischl fischl@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 > > > > > > > ayendiki@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, _andreia_@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 > > > > > > > > > > > > > > > > > > > > > > > ayendiki@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, _andreia_@sapo.pt wrote: > > > > > > > > > > > I'm using Centos5, which file should I > > > > > > > > > > > download? The one for > > > > > CentOS 6 or > 4? > > > > > > > Quoting Anastasia Yendiki > > > > > > > ayendiki@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, _andreia_@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 > > > > > > > > > > > > > > > > > > > > ayendiki@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, _andreia_@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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > fischl@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, > > > > > > > > > > > > _andreia_@sapo.pt > > > > > > > > > > > > > > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > Hi Bruce, > > > > > > > > > > > > > > Thank you for the quick response! > > > > > > > > > > > > > > In the meanwhile, does that also > > > > > > > > > > > > > > apply > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > to > > > > > > cortical > > > > > > > > > > > > > > > > > > > > > > > > > cortical > > > > > > > > > > > > > > > > > cortical > > > > > > > cortical > > > > > > > > > > > > > > > > > > > > > > > > > cortical > > > > > > > > > > thickness > > > > > > > > > > > > and > > > > > > > > > > > > volume? > > > > > > > > > > > > > > Thank you! > > > > > > > > > > > > > > Andreia > > > > > > > > > > > > > > Quoting Bruce Fischl > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > fischl@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, > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _andreia_@sapo.pt > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > Hi all, > > > > > > > > > > > > > > > > > > I'm using FS 5.0 and some > > > > > > > > > > > > > > > > > > time > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ago I > > > > > > was > > > > > > > > > > > > > > told by > > > > > > > > > > > was > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > was > > > > > > > > > > > > > > was > > > > > > > > > > > > > > > was > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>> >>>>>> > > > > > > Bruce that I had > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > to > > > > > > > > > > > > > > threshold the BA in order to have > > > > > > > > > > > > > > an > > > > > > approximate > > > > > > > > > > area > > > > > > > > > > > > approximate > > > > > > > > > > > > > > > > > > > > > > > > > > approximate > > > > > > > > > > approximate > > > > > > > > > > > approximate > > > > > > > > > > > > > > > when > > > > > > > > > > > > > >>>>>>>>>>>>> overlaying > > > > > > > > > > > > > > in the inflated surface. To get > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > surface > > > > > > > > > > > > > > area > > > > > > values > > > > > > > > > > I > > > > > > > > > > > > > > values > > > > > > > > > > also > > > > > > > > > > > > > > > values > > > > > > > > > > values > > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > table > > > > > > > > > > > > > > table > > > > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > for > > > > > > > > > > > > statistical > > > > > > > > > > > > > for > > > > > > > > > > > > > for > > > > > > > > > > > > > > > > for > > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>> analysis > > > > > > > > > > > > > > since there are the thresolds > > > > > > > > > > > > > > issue. > > > > > > > > > > > > > > > > > > I want to study mainly > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > cortical > > > > > > thickness > > > > > > > > > > > > > > and > > > > > > > > > > thickness > > > > > > > > > > > > > > > > > > > > > > > > > > > > thickness > > > > > > > > > > > > > > > > thickness > > > > > > > thickness > > > > > > > > > > > > > > > > > > > > > > > > > > > > thickness > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > surface > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > area but > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > also > > > > > > > > > > > > > > look also at the volume (which is > > > > > > surface-based, > > > > > > > > > > thus > > > > > > > > > > > > > > thickness*surface are will not be > > > > > > > > > > > > > > = > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > volume > > > > > > since > > > > > > > > > > they > > > > > > > > > > > > > > since > > > > > > > > > > are > > > > > > > > since > > > > > > > since > > > > > > > > > > > > > > > > > > > an > > > > > > > > > > > > >>>>>>>>>>>>> > average > > > > > > > > > > > > > > from each label, right?). > > > > > > > > > > > > > > > > > > I' not sure of which > > > > > > > > > > > > > > > > > > approach > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > to > > > > > > follow > > > > > > > > > > > > > > now... > > > > > > > > > > follow > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > follow > > > > > > > > > > > > > > follow > > > > > > > > > > > > follow > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > > the > > > > > > > > > sent > > > > > > > > the > > > > > > > > > > the > > > > > > > > > > > > > > > > > > > > > > > > > to > > > > > > > > > > > > you in error > > > > > > > > > > > > > but does not contain patient > > > > > > > > > > > > > > > > > > > > > > > > > > > > information, > > > > > > please > > > > > > > > > contact > > > > > > > > > > > > > please > > > > > > > > > the > > > > > > > > please > > > > > > > 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 >