Re: [Freesurfer] Segmentation

[Bruce Fischl]

Hi Mehul,

We explicitly label ventricular CSF, but not sulcal CSF (which you pretty 
much can't do from only a T1 volume). The ICV would give you an 
approximation of the sum of it all, so yes I think what you are doing is a 
reasonable approach.

cheers,
Bruce

On Thu, 19 Jul 2007, Mehul Sampat 
wrote:

Hi

I am interested in measuring the Brain Parenchymal Fraction (BPF) which is
defined as follows:

BPF = (total White Matter (WM) Volume + total Gray Matter (GM) Volume) /
(total White Matter Volume (WM) + total Gray Matter Volume (GM)+ total CSF
volume)

I think I get the White and Gray Matter Volumes for each hemisphere from the
command: mris_anatomical_stats.
I think the  denominator in the BPF equation is just the Intracranial
Volume, reported in the aseg.stats file

Would this be an appropriate way to measure these volumes ?
Thanks
Mehul
p.s: For the subject bert the BPF = 1661478/1799364 = 0.92


On 6/25/07, Bruce Fischl <[EMAIL PROTECTED]> wrote:

Hi Antonio,

that's why we we use the surfaces for white matter and cortical gray
matter volume.

cheers,
Bruce
On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:

> Hi Bruce,
> Thank you for your quick response.
>
> Our problem, actually, is that when we visualize the aseg.mgz volume
> (with color-coded subcortical structures) we see that WM is classified
> as GM (left circle around insula in the figure) and GM is classified as
> WM (right lower circle in the figure).
> So, even if the surfaces look good, we are worried about the effects of
> this misclassification on volume measurements in aseg.mgz.
>
> Thanks,
>
> Antonio
>
>
>
>> -----Original Message-----
>> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
>> Sent: Monday, June 25, 2007 4:10 PM
>> To: Gallo, Antonio (NIH/NINDS) [F]
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Segmentation
>>
>> Hi Antonio,
>>
>> I wouldn't use the wm.mgz for much of anything. It's really just an
>> intermediate step in the creation of the surfaces. In general we trust
> the
>> ?h.white and ?h.pial surfaces first, then the aseg.mgz for things like
>> hippocampus, ventricles, etc...
>>
>> Bruce
>>
>>
>> On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
>>
>>> Hi All,
>>>
>>> Upon reviewing subortical segmentations I see that often a mismatch
>>> exists between what appears on the wm.mgz and the color-coded
> segmented
>>> maps.
>>>
>>> Precisely - as an example - in the attached figure you can see that
> in
>>> the case of left insula WM, part of the tissue was classified as GM
> (in
>>> brown) in the color-coded segmented map and as WM in the wm.mgz.
>>> Contrariwise, the right temporal-parietal GM cortex part of the
> tissue
>>> is classified as WM (in green) the color-coded segmented map and as
>>> non-WM in the wm.mgz. The latter occurs in many regions of the brain
>>> without a clear anatomical pattern.
>>>
>>>
>>>
>>> I was wondering if this is just a display issue or it rather reflects
>>> some mismatch in actual tissue classification with consequential
> errors
>>> in the generated values of thickness and volumes as well?
>>>
>>> If so, is there any way I can correct for this?
>>>
>>>
>>>
>>> Thank you in advance,
>>>
>>>
>>>
>>> Antonio
>>>
>>>
>>>
>>>
>>>
>>> Antonio Gallo, MD
>>>
>>> NIB-NINDS-NIH
>>>
>>> 10 Center Drive
>>>
>>> Building 10, Room 5B16
>>>
>>> Bethesda, MD, 20892 - USA
>>>
>>> ph #: 001-301-402.6391
>>>
>>> fax #: 001-301-402.0373
>>>
>>> ***********************
>>>
>>>
>>>
>>>
>
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