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