Hi Bruce,
That would be great. I'm aware of the difficulty in putting partial volume
information into segmentation, but maybe it could help to achieve other useful
information as aseg.stats only provides the total volume for each label.
Thanks,
Anthony
--- On Thu, 5/3/09, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] partial volume correction in mri_segstats
To: "Anthony" <slam_...@yahoo.com>
Cc: freesurfer@nmr.mgh.harvard.edu
Date: Thursday, 5 March, 2009, 11:04 AM
Hi Anthony,
we're happy to provide the code, but there's no easy way to get a mask,
since each border voxel has more than 1 label in it.
cheers,
Bruce
On Wed, 4 Mar 2009, Anthony wrote:
> Hi Bruce,
>
> Thanks a lot for your reply . Is there anyway that I can get a mask for a
certain class (e.g WM) after partial volume correction using FS ? Or is it
possible for you to provide more details of it so I can reproduce the
calculation to get the mask ?
>
> Anthony
>
> --- On Thu, 5/3/09, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] partial volume correction in mri_segstats
> To: "Anthony" <slam_...@yahoo.com>
> Cc: freesurfer@nmr.mgh.harvard.edu
> Date: Thursday, 5 March, 2009, 9:33 AM
>
> Hi Anthony,
>
> it should be more accurate (and more reliable in our studies). It
> estimates the volume fraction of each tissue class on the border of the
> structure, assuming it is mixed with adjacent classes by estimating the
> local mean of the two tissue classes, then computing the mixing
> coefficients that explain the observed intensity. Thus for example if you
> have a dark hippocampal voxel bordering ventricle it will compute that the
> voxel has a fair amount of ventricle in it.
>
> cheers,
> Bruce
>
>
> On Wed, 4 Mar 2009, Anthony wrote:
>
>> Hi all,
>>
>>
>>
>> In recon-all pipeline , mri_segstats runs with -pv mri/norm.mgz
>> option ,as written from
>> http://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats , it is used to
>> compensate partial voluming. I wonder what exactly does this do, as
the
> volumes given by aseg.stats are different from
>> aseg.mgz and why is it more accurate ? I will appreciate if anyone
could
> help to clarify this .
>>
>> Thanks
>>
>>
>>
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