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Along with normalizing for eTIV, we'd like to normalize regional cortical
volumes for total brain/tisuse volume (TBV).
Is the output BrainSegNotVent in the aseg.sats basically equivalent to TBV?
Jim
The materials i
Hello All,Does freesurfer generate a file with total brain volume after the recon-all procedure? Where can this be accessed?Thanks,AR.
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I would like to calculate total brain volume (defined as: total white,
gray, and subcortical altogether). Should I take the BrainSegVol and
minus out cerebellum and ventricles, or add the white and gray matter
volumes from mris_anatomical_stats (it seems I remember hearing that white
matter from m
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Hello Free Surfer developers,
>From my understanding, the volumes provided in the aseg.stats document is not
>corrected by the head size.
In order to do that, it is recommended to use the ITV and the label ID's:
mri_label_volume -eTIV \
$sdir/transf
Yes, if you exclude the ventricles
On 4/27/2020 6:03 PM, Alexopoulos, Dimitrios wrote:
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Along with normalizing for eTIV, we’d like to normalize regional
cortical volumes for total brain/tisuse volume (TBV).
Is the output *BrainSegNotVent *in the aseg.sats
On Behalf Of Douglas N. Greve
Sent: Monday, April 27, 2020 7:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] total brain volume
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Yes, if you exclude the ventricles
On 4/27/2020 6:03 PM, Alexopoulos, Dimitrios wrote:
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Hi Anil,
There are two values in the aseg.stats file - BrainMaskVOl and
BrainSegVol. BrainMaskVol is the volume of all the voxels that are
included in the brainmask.mgz volume. BrainSegVol is the volume of all
the voxels that are labeled in the aseg.mgz segmentation.
--
Jenni Pacheco, M.A.
There's also an estimated total intracranial volume (eTIV) in
aseg.stats -- not the same thing as brain volume but close enough that
you might be interested.
doug
Jenni Pacheco wrote:
Hi Anil,
There are two values in the aseg.stats file - BrainMaskVOl and
BrainSegVol. BrainMaskVol is
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are
quiet a bit more so. We have a new tool for generating the estimate of the
gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I
think Doug or Nick has integrated it into the dev version of
Bruce,
So if I downloaded the dev version of the program I could use it to get
the volumes from subjects processed with 3.0.3? And would adding these
volumes together generate the total volume I'm looking for (including
subcoritical)? Thanks!
-Derin
> Hi Derin,
>
> the aseg labeling of cortica
you would need to add in whatever subcortical components you wanted to
include, as they are excluded from the wm volume
On Fri, 2 Feb 2007, Derin
Cobia wrote:
Bruce,
So if I downloaded the dev version of the program I could use it to get
the volumes from subjects processed with 3.0.3? And wo
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 2007, Bruce Fischl wrote:
you would need to add in whatever subcortical components you wanted to
include, as they are excluded from the wm volume
On Fri, 2 Feb 2007, Derin Cobia wrote:
Bruce,
So if I downloaded the dev vers
Is there any way I can get mris_wm_volume? If not, what's the next best
thing? Can I use the aseg.stats estimates?
-Derin
>
> I have not implemented it in recon-all yet.
>
> doug
>
>
>
>
> On Fri, 2 Feb 2007, Bruce Fischl wrote:
>
>> you would need to add in whatever subcortical components you
sure. Tell us what platform and Nick can post it for you
On Mon, 5 Feb 2007,
Derin Cobia wrote:
Is there any way I can get mris_wm_volume? If not, what's the next best
thing? Can I use the aseg.stats estimates?
-Derin
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 20
CentOS 4 (32-bit). Thanks!
-Derin
> sure. Tell us what platform and Nick can post it for you
> On Mon, 5 Feb 2007,
> Derin Cobia wrote:
>
>> Is there any way I can get mris_wm_volume? If not, what's the next best
>> thing? Can I use the aseg.stats estimates?
>>
>> -Derin
>>
>>>
>>> I have not
Derin,
mris_wm_volume for 32bit centos is on the website:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
It's gzipped, so to install, after downloading and copying to your
$FREESURFER_HOME/bin, type:
gunzip mris_wm_volume.gz
chmod a+z mris_wm_volume
Typing 'mris_wm_volume' without args gives
I've noticed that the gray matter volume output from mris_anatomical_stats
(lh) vs. mris_volume (lh.pial) differs. Am I missing something? Do I
need to run mris_volume for a different surface? Thanks.
-Derin
> sure. Tell us what platform and Nick can post it for you
> On Mon, 5 Feb 2007,
> Der
Hello,
I was curious if anyone had specific recommendations for correcting ROIs
for total brain volume/ICV. From what I can tell, some groups correct each
ROI by computing a ratio of ROI/total_brain_volume. Other groups, however,
enter total brain volume as a covariate in their statistical mod
No, this was a situation that we were not anticipating. You'll have to
do it yourself. If you run asegstats2table, it will create a table that
has the BrainSegNotVet and the eTIV
On 9/1/2021 4:19 PM, Fabiola Macruz wrote:
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Not sure if this went through the first time yesterday, here it is again.
Thanks.
I've noticed that the gray matter volume output from mris_anatomical_stats
(lh) vs. mris_volume (lh.pial) differs. Am I missing something? Do I
need to run mris_volume for a different surface? Thanks.
-Derin
you would need to subtract the ?h.white volume from the ?h.pial to get
gm volume
On Tue, 6 Feb 2007, Derin Cobia wrote:
Not sure if this went through the first time yesterday, here it is again.
Thanks.
I've noticed that the gray matter volume output from mris_anatomical_stats
(lh) vs. mris_v
Then is there a reason to use mris_volume when I can just do
mris_anatomical_stats and forget the math?
So, if I take the ?h.pial volume then add in the subcortical structure
volumes from aseg.stats (as you mentioned earlier) then that would give me
the estimated whole brain volume? Thanks Bruce!
is whole brain volume all you care about?
On Tue, 6 Feb 2007, Derin Cobia
wrote:
Then is there a reason to use mris_volume when I can just do
mris_anatomical_stats and forget the math?
So, if I take the ?h.pial volume then add in the subcortical structure
volumes from aseg.stats (as you menti
For one of our projects. We're using cortical gray matter for another
(which I wanted to clarify).
-Derin
> On Tue, 6 Feb 2007, Derin Cobia
> wrote:
>
>> Then is there a reason to use mris_volume when I can just do
>> mris_anatomical_stats and forget the math?
>>
>> So, if I take the ?h.pial vol
Hi Derin,
so I guess I would use brain volume as the surface volumes of the gray
and the white + subcortical volumes (and cerebellum).
Bruce
On Tue, 6 Feb 2007, Derin Cobia wrote:
For one of our projects. We're using cortical gray matter for another
(which I wanted to clarify).
-Derin
Hello all,I have two questions here:1. The summation of all the structure volumes listed in the aseg.stats seems to exceed the Brain Segmentation Volume given in the same file. With the exclusion of CSF and ventricles, the number becomes smaller than the Brain Segmentation Volume. If I am to study
[EMAIL PROTECTED] wrote:
Hello all,
I have two questions here:
1. The summation of all the structure volumes listed in the aseg.stats
seems to exceed the Brain Segmentation Volume given in the same file.
With the exclusion of CSF and ventricles, the number becomes smaller
than the Brain S
Hello,
We would like to calculate a Total Brain Volume based on data in aseg.stat
generated from version 5.1.0. Can I use intra crainal volume as estimated for
total brain volume? Or should I just add total grey volume with subcortical
grey volume with total white matter volume?
Thanks,
Knu
Hi Knut, you can copy the following file into
$FREESURFER_HOME/bin/mri_segstats
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
(assuming you're using linux)
The run
recon-all -segstats -s subject
This will create a new aseg.stats file with total brain volume based
Subject: Re: [Freesurfer] total brain volume or intra crainal volume as
> estimated for total brain volume
>
> Hi Knut, you can copy the following file into
> $FREESURFER_HOME/bin/mri_segstats
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
> (assuming
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