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 > > > > > > >
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> > > > > > > > > > > > > > > > > >
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_andreia_＠sapo.pt