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