Hi Doug,
Ok, you're going to make me work for it! :)
I'm guessing that XhpialvolTot in that formula is simply the output of
`mris_volume Xh.pial` ?
What I'm confused about is why the sum of TotalGrayVol +
CorticalWhiteMatterVol seems to be about 8-10% larger than
SupraTentorialVol. (And that's even after including ventricles into the
SupraTentorialVol calculation...)
thanks,
-MH
On Tue, 2012-02-21 at 13:56 -0500, Douglas N Greve wrote:
> Hi Mike, below is the code that we use. Let me know if it is not clear.
> doug
>
>
> SupraTentVolCor = SupraTentorialVolCorrection(mri_aseg, mri_ribbon);
> SupraTentVol = SupraTentVolCor + lhpialvolTot + rhpialvolTot;
>
> /*!
> \fn double SupraTentorialVolCorrection(MRI *aseg, MRI *ribbon)
> \brief Returns the volume of supratentorial structures that do not
> fall inside the pial surface or are cut by the pial surface. The idea
> is that the volume of everything in the pial surface can be computed
> using the surface and that this function can be used to compute
> everything else. Note that there is no partial volume correction.
> \param aseg - aseg.mgz or aparc+aseg.mgz
> \param ribbon is the ribbon.mgz, which has non-zero values for
> everything inside the pial surf.
> */
> double SupraTentorialVolCorrection(MRI *aseg, MRI *ribbon)
> {
> int c,r,s,SegId;
> double vol = 0;
> int RibbonVal, VoxSize;
>
> VoxSize = aseg->xsize * aseg->ysize * aseg->zsize;
> for(c=0; c < aseg->width; c++){
> for(r=0; r < aseg->height; r++){
> for(s=0; s < aseg->depth; s++){
>
> // If this voxel is inside the pial, then skip it because it
> // will be part of the surface-based volume measure
> RibbonVal = MRIgetVoxVal(ribbon,c,r,s,0);
> if(RibbonVal == 0) continue;
>
> // If it gets here, it means that the voxel was not within
> // the pial surface. It could be in a structure that should
> // be part of the supratentorium.
>
> // These are midline, medial wall, or unknown structures
> // that the pial could cut through.
> SegId = MRIgetVoxVal(aseg,c,r,s,0);
> if(SegId == Left_Lateral_Ventricles) vol += VoxSize;
> if(SegId == Right_Lateral_Ventricles) vol += VoxSize;
> if(SegId == Left_choroid_plexus) vol += VoxSize;
> if(SegId == Right_choroid_plexus) vol += VoxSize;
> if(SegId == Left_Inf_Lat_Vent) vol += VoxSize;
> if(SegId == Right_Inf_Lat_Vent) vol += VoxSize;
> if(SegId == WM_hypointensities) vol += VoxSize;
> if(SegId == Left_WM_hypointensities) vol += VoxSize;
> if(SegId == Right_WM_hypointensities) vol += VoxSize;
> if(SegId == Left_Thalamus_Proper) vol += VoxSize;
> if(SegId == Right_Thalamus_Proper) vol += VoxSize;
> if(SegId == Left_Thalamus) vol += VoxSize;
> if(SegId == Right_Thalamus) vol += VoxSize;
> if(SegId == CC_Posterior) vol += VoxSize;
> if(SegId == CC_Mid_Posterior) vol += VoxSize;
> if(SegId == CC_Central) vol += VoxSize;
> if(SegId == CC_Mid_Anterior) vol += VoxSize;
> if(SegId == CC_Anterior) vol += VoxSize;
> if(SegId == Left_VentralDC) vol += VoxSize;
> if(SegId == Right_VentralDC) vol += VoxSize;
>
> // These are unlikely to have the pial surface cut through
> // them, but no harm to include them
> if(SegId == Left_Caudate) vol += VoxSize;
> if(SegId == Right_Caudate) vol += VoxSize;
> if(SegId == Left_Putamen ) vol += VoxSize;
> if(SegId == Right_Putamen ) vol += VoxSize;
> if(SegId == Left_Pallidum) vol += VoxSize;
> if(SegId == Right_Pallidum) vol += VoxSize;
> if(SegId == Left_Hippocampus) vol += VoxSize;
> if(SegId == Right_Hippocampus) vol += VoxSize;
> if(SegId == Left_Amygdala) vol += VoxSize;
> if(SegId == Right_Amygdala) vol += VoxSize;
> if(SegId == Left_Accumbens_area) vol += VoxSize;
> if(SegId == Right_Accumbens_area) vol += VoxSize;
> }
> }
> }
> return(vol);
> }
>
>
> Michael Harms wrote:
> > Hi Doug or Nick,
> > I was wondering if you could clarify once exactly how the SupraTentorial
> > volume in the aseg.stats is calculated from an algorithmic perspective.
> > In particular, it isn't simply the sum of CortexVol +
> > CorticalWhiteMatterVol + SubCortGrayVol, as implied by the Wiki.
> >
> > thanks!
> > -MH
> >
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
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