On Sat, Sep 13, 2014 at 3:27 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> 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 measures of the pial surface as will the SurfArea, MeanCurv, GausCurv, FoldInd, and CurvInd fields for each ROI (thickness and number of vertices will stay the same)

doug

On 09/11/2014 07:29 PM, will brown wrote:

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 at 9:11 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:

sorry, this thread has gotten too deep. Can someone summarize the
question?

On Thu, 11 Sep 2014, _andreia_@sapo.pt <mailto:andreia_@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 <willbrown1987@gmail.com
<mailto:willbrown1987@gmail.com>>:

Thanks again, for the record, I'm using freesurfer
version 5.3.0
on Centos 6.

On 9/09/2014 11:00 PM, <_andreia_@sapo.pt
<mailto:andreia_@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
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 surface area for each
hemisphere without including, for example, the pial
surface that you see in the hippocampus which is not
accurate and one should not care about. In the end,
the second set gives you the sum of the areas in
aparc, thus, you can just make a sum of that
parcellation if you want. I just realized that.

2) No. In the new stats file, the value that you
want is at the bottom:

# ColHeaders StructName NumVert SurfArea GrayVol
ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

And when running aparcstats2table that's the value
you should get in the table. I think that # Measure
Cortex, WhiteSurfArea, White Surface Total Area may
be including more stuff since it is bigger.

If what you want is only the total hemisphere
surface area you only need to run the second set of
commands. If you want the area of each DK altas
parcellation then run the first set and then simply
add them to get total hemisphere surface area.

Someone from Freesurfer staff will correct me if I'm
wrong. (Please) I'm Ccing Doug since he was replying
to your previous emails.

Let's wait for their feedback.

Andreia

Citando will brown <willbrown1987@gmail.com
<mailto:willbrown1987@gmail.com>>:

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
provide the pial boundary stats for the whole brain rather
than just cortex?

2) The surface area value that I am looking for (grey
matter surface area at the grey/pial boundary) is listed
in the new stats table next to: # Measure Cortex,
WhiteSurfArea, White Surface Total Area, ?

Thanks again,
Will

On Tue, Sep 9, 2014 at 5:36 PM, will brown
<willbrown1987@gmail.com <mailto:willbrown1987@gmail.com>> wrote:
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.
Will

On Wed, Sep 3, 2014 at 1:12 AM, <_andreia_@sapo.pt
<mailto:andreia_@sapo.pt>>

wrote:

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 -mgz -cortex
../label/rh.cortex.label -f
../stats/rh.aparc.pial.stats -b -a
../label/rh.aparc.annot -c
../label/aparc.annot.ctab SUBJ rh pial

Then run aparcstats2table using
aparc.pial instead of aparc (only
because I called this new parcellation
aparc.pial)

To get the total surface area of each
hemisphere I use:

In the subject stats dir:

mris_anatomical_stats -l
../label/lh.cortex.label -f
lh.total_pial.stats -b SUBJ lh pial

mris_anatomical_stats -l
../label/rh.cortex.label -f
rh.total_pial.stats -b SUBJ rh pial

Then run aparcstats2table using
total_pial instead of aparc (again, only
because I called this new parcellation
total_pial. You may call it whatever
you'd like)

Just remeber to leave the specified dirs
when creating the tables. If you dont't
I think they will be created in the
current dir.

I use FS 5.0.

Is this what you want?

Best,
Andreia

Citando will brown
<willbrown1987@gmail.com <mailto:willbrown1987@gmail.com>>:

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, XXXX, mm^2

How about the gray matter?

Thanks,
Will

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