surfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, November 8, 2021 1:40:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Brain Volume Extraction
You could run it up to the skull stripping (-autorecon1), then compute the
brain volume yourself from the
You could run it up to the skull stripping (-autorecon1), then compute
the brain volume yourself from the skull-stripped image. You could also
use samseg; samseg only takes an hour or so to run and outputs a measure
of total intracranial volume, but you could also extract total brain
volume fro
Depends on how you define "brain volume". If you're using BET, then I
assume that you are just counting the number of voxels in the mask? If
so, you can use mri_binarize and use the --count countfile to give you a
count of the voxels.
doug
On 09/22/2012 08:22 PM, Ana Arruda wrote:
>
> I've j
I've just seen the output from mri_watershed. And from the file aseg.stats,
is there any measure that provide the brain volume?
Thank you once again,
Ana Arruda
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Thank you.
But in the last message I forgot to say my final aim. After the skull
stripping, how can I measure the volume?
Ana Arruda
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Hi Ana
the binary mri_watershed does skull stripping in FreeSurfer.
cheers
Bruce
On Sun, 23 Sep
2012, Ana Arruda wrote:
Hi,
I've been working with Freesurfer and FSL in order to compare the two
softwares. However the last one has a tool called "Brain Extraction Tool"
(BET) that provides all
Thanks Doug. And good question that I've wondered about myself Jeff.
The part about the high-resolution volume that is created "under the
hood" explains why mris_wm_volume takes substantially longer to complete
than would be expected relative to just running `mris_volume Xh.white`
and then subtr
Hi Jeff, it's going to be tricker than that to get the exact value. For
the WM volume computation, there's yet another routine that is used.
This one creates a high-resolution volume to determine which voxels are
withing the WM surface. It then loops through the voxels within the WM
surface and
Thank you Doug for your answer. After reading the wiki more, it has led me
to another question.
I am trying to duplicate the White Matter value from aseg.stats using
FreeSurfer 5.0.0. The value from aseg.stats is 220804 (as it is also when
running mris_wm_volume). By hand, when I run mris_volum
, 2011 11:46 AM
> To: Jeff Sadino
> Cc: andrei.sherstyuk; skoga...@gmail.com; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Brain Volume measures
>
> Hi Jeff, the total cortical gray matter is based on the volume between
> the white and pial surfaces. The other s
Hi Jeff, the total cortical gray matter is based on the volume between
the white and pial surfaces. The other structures you mention below are
based on the automatic volume segmentation.
doug
Jeff Sadino wrote:
> Hello,
>
> Thank you Bruce and Doug for your answers to my previous question
> abo
Hi Adam, try rescaling the brain volume to be around 1 (demeaning it
might help too). The next version of FS will remove these scaling problems.
doug
Adam David Felton wrote:
> Hello,
>
> I am using Qdec to analyze thickness (etc) using various IVs (e.g.,
> Verbal IQ) while controlling for cor
Hi Alan,
I'd say it depends on what the study is about, but in principle, I'd
think that the covariates should remove what would have potential to be
confounding more what the main effect would be. In the example of
schizophrenia, I'd choose BrainSegVolNotVent, and run both models, with
and w
Hi Anderson:
Your explanation is very well put. I have a question. Suppose one is looking
at High Risk datasets (for example Schizophrenia) where the
brain morphological alterations are subtle but spread across the brain,
which covariate would you use?
thanks,
Alan
[Beth Israel Deaconess Medica
A side note: If you are using FS 4.5.0 or earlier, there is also
BrainSegVolNotVent, which discount ventricles. If you want to capture
effects of aging or atrophy, perhaps this could be more sensitive than
BrainSegVol.
On 24/08/11 12:32, Anderson Winkler wrote:
Hi Zuzana,
Yes, you can use Br
Hi Zuzana,
Yes, you can use BrainSegVol as a measurement of brain volume (I'd
assume you are using FS <=4.5.0). Note that there is another measurement
that you might be interested in, the IntraCranialVol. These measurements
tell different things and not necessarily correlate well one with
ano
Hi Justin,
It partly depends on what exactly you want when you say "brain volume".
Do you want a measure of estimated intracranial volume (intended to be
independent of atrophy)? A measure of gray matter + white matter +
ventricles? Or only gray matter + white matter? Do you care whether
the ce
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