Dear All,
We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and analyzed with FS 3.0.5.
Images belong to a group of Multiple Sclerosis patients.
We would like to ask some questions and we apologize for the fact that we have quite a number of them :-)
First, regarding measurements coming from mris_anatomical_stats:
1) What is exactly included in total WM volume?
2) Is total WM volume the sum of left and right WM hemisphere or just the WM volume from the side we specify (but if this is case, why we got the same values after running mris_anatomical_stats for lh and rh hemisphere) ?
3) Since there are many WM lesions (with many juxta-cortical lesions that need manual editing), we were wondering if total WM volume does include the WM hypointensities as well or those are just treated separately.
4) Does the total GM volume include the volume of the subcortical structures and cerebellum or just refer to the cortical GM volume?
Second, some other questions on the aseg.stat file:
1) What is exactly included in CSF label? Does it comprehend the CSF in the ventricles + the sulcal CSF, or just the the sulcal CSF?
2) Does the volume of the WM hypointensities manually edited (which happens very often with MS lesions close to the cortex) end up in the WM hypointensities volume?
Last, as we are interested in measuring subjects' BPF, we were wondering which would be the best way to compute it?
Thanks a lot 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
***********************
On Thu, 25 Oct 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Dear All,
We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and analyzed with FS 3.0.5.
Images belong to a group of Multiple Sclerosis patients.
We would like to ask some questions and we apologize for the fact that we have quite a number of them :-)
First, regarding measurements coming from mris_anatomical_stats:
What is exactly included in total WM volume?
in mris_anatomical_stats this is the total volume occupied by voxels in the wm.mgz volume that are "on". We now use mris_wm_volume to compute the volume using the surfaces, which we believe is more accurate.
Is total WM volume the sum of left and right WM hemisphere orjust the WM volume from the side we specify (but if this is case, why we got the same values after running mris_anatomical_stats for lh and rh hemisphere) ?
there is no lateralization in this calculation, but you could use the aseg.mgz to get lh and rh volumes (in the aseg.stats file)
Since there are many WM lesions (with many juxta-corticallesions that need manual editing), we were wondering if total WM volume does include the WM hypointensities as well or those are just treated separately.
it depends whether they were classified as wm in the wm.mgz. If you use the mris_wm_volume method, then the hypointensities *will* be included in the volume.
Does the total GM volume include the volume of the subcorticalstructures and cerebellum or just refer to the cortical GM volume?
just cortical GM.
Second, some other questions on the aseg.stat file:
What is exactly included in CSF label? Does it comprehend theCSF in the ventricles + the sulcal CSF, or just the the sulcal CSF?
CSF is sulcal CSF and we don't label very much of it, as you can't really see it well on a T1-weighted MRI. The ventricles have their volumes given individually.
Does the volume of the WM hypointensities manually edited(which happens very often with MS lesions close to the cortex) end up in the WM hypointensities volume?
if they are labeled as hypointensities in the aseg.mgz. Are you manually editing them there or in the wm.mgz?
Last, as we are interested in measuring subjects' BPF, we were wondering which would be the best way to compute it?
Thanks a lot 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
Hi Bruce,
Thanks for your prompt reply.
Could you please further clarify some points below ?
-----Original Message-----
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]
Sent: Thursday, October 25, 2007 8:38 PM
To: Gallo, Antonio (NIH/NINDS) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] WM volume & CSF & BPF
On Thu, 25 Oct 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Dear All,
We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and
analyzed with FS 3.0.5.
Images belong to a group of Multiple Sclerosis patients.
We would like to ask some questions and we apologize for the fact
that
we have quite a number of them :-)
First, regarding measurements coming from mris_anatomical_stats:
What is exactly included in total WM volume?
in mris_anatomical_stats this is the total volume occupied by voxels in
the
wm.mgz volume that are "on". We now use mris_wm_volume to compute the
volume using the surfaces, which we believe is more accurate.
In WM.mgz file I can see "on" ventricles, deep nuclei, brainstem and "off" (zeroed) some little spots that don't correspond to WM lesions and are not enclosed by any surface contour (so we didn't correct).
Since we would like to stay on FS 3.0.5, at least for now, could you please better clarify what does WM volume refer to?
Is total WM volume the sum of left and right WM hemisphere
or
just the WM volume from the side we specify (but if this is case, why
we
got the same values after running mris_anatomical_stats for lh and rh
hemisphere) ?
there is no lateralization in this calculation, but you could use the
aseg.mgz to get lh and rh volumes (in the aseg.stats file)
Since there are many WM lesions (with many juxta-cortical
lesions that need manual editing), we were wondering if total WM
volume
does include the WM hypointensities as well or those are just treated
separately.
it depends whether they were classified as wm in the wm.mgz. If you use
the
mris_wm_volume method, then the hypointensities *will* be included in
the
volume.
Does the total GM volume include the volume of the
subcortical
structures and cerebellum or just refer to the cortical GM volume?
just cortical GM.
Second, some other questions on the aseg.stat file:
What is exactly included in CSF label? Does it comprehend
the
CSF in the ventricles + the sulcal CSF, or just the the sulcal CSF?
CSF is sulcal CSF and we don't label very much of it, as you can't
really
see it well on a T1-weighted MRI. The ventricles have their volumes
given
individually.
Does the volume of the WM hypointensities manually edited
(which happens very often with MS lesions close to the cortex) end up
in
the WM hypointensities volume?
if they are labeled as hypointensities in the aseg.mgz. Are you
manually
editing them there or in the wm.mgz?
We use to edit the WM lesions (mainly for the ones close to the cortex) by using control points and checking that the ?h.white looks fine (staying at the edge of the lesion and not inside.
Should we correct the WM lesions differently?
Last, as we are interested in measuring subjects' BPF, we were
wondering
which would be the best way to compute it?
Could you suggest to us the best way to compute the BPF ?
Thanks a lot in advance, (again)
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Gallo, Antonio (NIH/NINDS) [F]