Hi Bruce, Thanks for your prompt reply.
Could you please further clarify some points below ? >-----Original Message----- >From: Bruce Fischl [mailto:[EMAIL PROTECTED] >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: >> >> 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. 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? > >> 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? 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 >> >> *********************** >> >> >> >>
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