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