Re: [Freesurfer] Brain Volume Extraction

2021-11-08 Thread Mohanad Arafe
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

Re: [Freesurfer] Brain Volume Extraction

2021-11-08 Thread Douglas N. Greve
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

Re: [Freesurfer] Brain Volume

2012-09-25 Thread Douglas N Greve
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

Re: [Freesurfer] Brain Volume

2012-09-22 Thread Ana Arruda
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/

Re: [Freesurfer] Brain Volume

2012-09-22 Thread Ana Arruda
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Brain Volume

2012-09-22 Thread Bruce Fischl
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

Re: [Freesurfer] Brain Volume measures

2011-12-02 Thread Michael Harms
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

Re: [Freesurfer] Brain Volume measures

2011-12-02 Thread Douglas N Greve
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

Re: [Freesurfer] Brain Volume measures

2011-12-01 Thread Jeff Sadino
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

Re: [Freesurfer] Brain Volume measures

2011-11-30 Thread Douglas N Greve
, 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

Re: [Freesurfer] Brain Volume measures

2011-11-30 Thread Douglas N Greve
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

Re: [Freesurfer] Brain volume covariate problem in QDEC

2011-09-16 Thread Douglas N Greve
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

Re: [Freesurfer] Brain volume in FreeSurfer analysis

2011-08-24 Thread Anderson Winkler
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

Re: [Freesurfer] Brain volume in FreeSurfer analysis

2011-08-24 Thread Alan Francis
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

Re: [Freesurfer] Brain volume in FreeSurfer analysis

2011-08-24 Thread Anderson Winkler
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

Re: [Freesurfer] Brain volume in FreeSurfer analysis

2011-08-24 Thread Anderson Winkler
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

Re: [Freesurfer] Brain Volume

2011-01-26 Thread Michael Harms
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