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 > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>> >>>>>> > > > > 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. 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