correct, unfortunately, the "White" label is hard coded into the program.
On 09/14/2014 02:24 AM, will brown wrote:
> Thanks Doug,
>
> Just to double check I understand you correctly, where the output says
> "# Measure Cortex, WhiteSurfArea, White Surface Total Area" this is
> now the surface ar
Thanks Doug,
Just to double check I understand you correctly, where the output says "#
Measure Cortex, WhiteSurfArea, White Surface Total Area" this is now the
surface area of the pial surface even though it is labeled White?
Cheers,
Will
On Sat, Sep 13, 2014 at 3:27 AM, Douglas N Greve
wrote:
You can run something like
cd $SUBJECTS_DIR/subject
mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c
label/aparc.annot.ctab subject lh pial
The "Measure Cortex" fields in the output stats/lh.aparc.pial.stats will
be measure
Sure. We'd like to know how to find the surface area of the cortical grey
matter from the pial surface. So specifically, what is the surface area of
the pial/grey matter boundary of the cortex for each hemisphere?
We're using Freesurfer v5.3 on Centos 6.
Thanks,
Will Brown
On Fri, Sep 12, 2014
sorry, this thread has gotten too deep. Can someone summarize the question?
On Thu, 11 Sep 2014, _andre...@sapo.pt wrote:
Ok. Then, I'm not sure if everything is correct with the command lines since
I use 5.0.
Any thought on this Freesurfer team?
Thanks,
Andreia
Citando will brown :
Ok. Then, I'm not sure if everything is correct with the command lines
since I use 5.0.
Any thought on this Freesurfer team?
Thanks,
Andreia
Citando will brown :
Thanks again, for the record, I'm using freesurfer version 5.3.0 on
Centos 6.
On 9/09/2014 11:00 PM, <_andre...@sapo.pt> wrote:
Thanks again, for the record, I'm using freesurfer version 5.3.0 on Centos
6.
On 9/09/2014 11:00 PM, <_andre...@sapo.pt> wrote:
> Hi Will,
>
> Just to clarify, what version of FS are you using? I think it might not be
> 5.0 and I don't know if everything aplies if we are using different
> version
Hi Will,
Just to clarify, what version of FS are you using? I think it might not be
5.0 and I don't know if everything aplies if we are using different
versions.
1) Yes, it is only based on the pial surface (and these command lines are
for the aparc, DK altas). The second set provides the surfac
Thanks Andreia, this does appear to have worked. Please forgive my
ignorance but I do just want to double check two things;
1) The first commands you have given provide the stats for the two
hemispheres of the cerebral cortex only based on the pial surface, whereas
the second set of commands provi
Thanks very much Andreia, yes this does look like what I want. I haven't
had a chance to test it yet but it does indeed appear to answer my
question. Thanks to those that have offered answers, to clarify, I did
indeed mean the surface area of the pial surface rather than the white/grey
boundary.
W
cortical gray
matter as ?.aparc.stats file only report WhiteSurfArea.
Thanks,
Will
Message: 17
Date: Wed, 27 Aug 2014 00:48:29 -0400
From: Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical gray matter surface area
To: freesurfer@nmr.mgh.ha
That is the surface area of the cortical GM where it has its junction
with the WM. Or do you want the surface area of the pial surface?
On 9/2/14 12:22 AM, will brown wrote:
Hi all,
I messed up this question recently so just want to clarify and try
again. We want to know the cortical gray
Hi Will,
I use the following commands to get surface area from the pial surface:
In the subject label dir:
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.APARC.PIAL.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab SUBJ lh pial
mris_anatomical_stats
] Cortical gray matter surface area
Hi all,
I messed up this question recently so just want to clarify and try again. We
want to know the cortical gray matter surface area of our subjects but are
unclear about how to get this info.
?.aparc.stats reports:
Measure Cortex, WhiteSurfArea, White Surface
Hi all,
I messed up this question recently so just want to clarify and try again.
We want to know the cortical gray matter surface area of our subjects but
are unclear about how to get this info.
?.aparc.stats reports:
Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2
How abou
: [Freesurfer] Cortical gray matter surface area
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <53fd631d.4070...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
The volume for each structure is given as the 4th column. If you want
total GM volume, look in aseg.stats
dou
The volume for each structure is given as the 4th column. If you want
total GM volume, look in aseg.stats
doug
On 8/26/14 8:43 PM, will brown wrote:
Hi all,
I am a little unclear as to how to find the cortical grey matter
volume in the stats output files. The ?.aparc.stats file shows:
Me
Hi all,
I am a little unclear as to how to find the cortical grey matter volume in
the stats output files. The ?.aparc.stats file shows:
Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2
What about grey?
Thanks,
Will
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