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
> > > > > > > > > > > > > > > > > > > > > > > >
> > > > > > > > _______________________________________________
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