Hi Doug,
I'm sorry about using the term "subcortical white matter". It
was due to misunderstanding your response, viz.
"the white matter volume computed from the pial-white
includes subcortical structures".
It's settled now, see response by Michael Harms and
my reponse to that.
Ed
On 4 Nov 2010,
Hi Ed,
What do you mean by subcortical white matter? Do you mean cerebellar
white matter? The mris_volume command will give you the entire volume
inside the white surface, which will include all gray matter structures.
This will not include cerebellar white matter.
doug
Ed Gronenschild wrote:
Hi Michael,
Thanks for your explanation. It was rather confusing
but the picture is now clear:
for the total cerebral white matter I should take the
measure "CorticalWhiteMatter" in the aseg.stats.
Ed
On 4 Nov 2010, at 15:05, Michael Harms wrote:
>
> Hi Ed,
> Is there a distinction in FreeSurf
Hi Ed,
Is there a distinction in FreeSurfer between "cortical" and
"subcortical" white matter? I thought that white matter was simply
white matter...
You wrote that the white matter values in aseg.stats are identical to
the output of mris_wm_volume, which is exactly what I would expect.
You do
Hi Doug,
This thread about GM and WM volumes was initiated by my question
on how to get the total cerebral GM and WM volumes.
From what I understand now is that for the GM I should take the
volume named "TotalGray" in the aseg.stats file. In the example
below that would be 710389.282729.
Howeve
Freesurfers,
So you can ignore this last question. I double-checked my addition and got
1046270 for the sum of all structures which is indeed more than
BrainSegNotVent. Oops.
Chris
On Nov 3 2010, bell0...@umn.edu wrote:
>
>
>One other thing. I did the addition of all the structures in aseg a
One other thing. I did the addition of all the structures in aseg and
am a bit confused. Here are the numbers for one subject.
BrainSeg= 1035602
BrainSegNotVent= 1034954
These two are almost identical but that is most likely due to the
lack of pv correction in BrainSeg, so I think that makes se
I had a question about gray matter and white matter volumes in FreeSurfer
version 4.5. Sorry, we have too many subjects to rerun easily through 5.0.
There is no gray matter listed in aseg.stats in 4.5. The two options I see
are using mris_volume or summing the aparc gray matter structures, are
Ah, the "white matter" volume computed from the pial-white includes the
subcortical structures. Once those are subtracted, you should get the #s
in the aseg.stats file.
doug
Ed Gronenschild wrote:
> Hi Doug,
>
> I checked the numbers again and found the difference:
>
> The last occurrence in th
Hi Doug,
I checked the numbers again and found the difference:
The last occurrence in the recon-all.log reads:
Getting Cerebral WM volumes from surface
lh white matter volume 251139
rh white matter volume 254730
Getting Cerebral GM and WM volumes from surfaces
lh surface-based volumes (mm3): wTo
Hi Ed, I can't replicate this. Can you double check your numbers again?
In particular, can you compare them against numbers that are printed in
the recon-all.log file?
In recon-all.log, look for the lines
Getting Cerebral GM and WM volumes from surfaces
lh surface-based volumes (mm3): wTo
Ed, can you send the recon-all.log file? The underlying code for
mris_volume and the program that creates the stats file is identical.
This other program (mri_segstats) prints out the values for the volumes
inside the lh.pial, etc, and this will be captured by the recon-all.log
file.
doug
Ed
Nope - the subcortical structures are all gm.
Allison
--
On Wed, 27 Oct 2010, Ed Gronenschild wrote:
> Hi Allison,
>
> Thanks.
> It is still confusing: for the gm the aseg.stats lists cortical as
> well as subcortical and the total volumes (being the sum of both).
> But for wm only cortical vol
Hi Allison,
Thanks.
It is still confusing: for the gm the aseg.stats lists cortical as
well as subcortical and the total volumes (being the sum of both).
But for wm only cortical volumes are present. Is there no
subcortical wm volume present or defined?
Ed
On 27 Oct 2010, at 15:58, Allison Stev
Ed,
I would use the values in the aseg.stats. I'm not sure why there is this
difference (Doug might be able to elaborate on how the values in
aseg.stats are calculated) but for v5.0, we went over how all the stats
were being calculated and make sure the values in the aseg.stats were the
most ac
Dear Bruce/Allison,
Could you please try to give response to my question
which wm and gm volumes I shoud use, see my
today's submission below.
Ed
On 27 Oct 2010, at 14:41, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Dear Christian,
Thanks for your suggestion. I followed the instructions to
Dear Christian,
Thanks for your suggestion. I followed the instructions to derive the
GM and WM volumes. Here are the (rounded-off) results for one example:
mris_volume lh.pial: 532767
mris_volume rh.pial: 536127
mris_wm_volume lh: 251139
mris_wm_volume rh: 254730
Accordingly:
gm lh = 532767 -
Dear Ed,
to my knowledge, "mris_wm_volume" is the best option to determine the
white matter volume.
See this wiki page for usage:
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
Best wishes,
Christian
---
Christian Scheel
Department of Psychiatry
University of Cologne
Am 26.10
Hi,
I post this once again because I didn't get any response.
In the v5.0.0 aseg.stats file I can find the following volumes:
- left/right cortical gray matter
- subcortical gray matter
- total cortical gray matter
- total gray matter volume
and
- left/right cortica
Hi,
In the v5.0.0 aseg.stats file I can find the following volumes:
- left/right cortical gray matter
- subcortical gray matter
- total cortical gray matter
- total gray matter volume
and
- left/right cortical white matter
- total cortical white matter
How can
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