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:

1.   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.

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) ?

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)

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.

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.

4.   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:

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?

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.

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?

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

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