[MINC-users] Estimating tissue volume from PVEs

[Andrew Reid]

Hello,

I want to get an estimate of tissue volume from the PVE volumes in my 
minc directories. As far as I can tell, this requires that I:

1. Mask with the brain mask (using Perl):

$mask = $subject_dir."/".$sname."/mask/".$prefix.$sname."_brain_mask.mnc";
`mincmath -mult ${volume} ${mask} ${temp_vol}`;

2. Resample with the inverse of the linear talairach transform:

$transform = 
$subject_dir."/".$sname."/transforms/linear/".$prefix.$sname."_t1_tal.xfm";
`mincresample -transformation ${transform} -tfm_input_sampling 
-invert_transformation ${temp_vol} ${temp_trans}`;

3. Calculate tissue volumes. For this I bin the volume into ranges of 
size 0.1, and multiply the resulting sum by the mid-point of the bin, 
adding two bins for [0:0.01] = 0 and [0.99:1] = 1. Then I sum the 
resulting values.

`mincstats -volume -quiet -range 
0.0,0.01,0.01,0.1,0.1,0.2,0.2,0.3,0.3,0.4,0.4,0.5,0.5,0.6,0.6,0.7,0.7,0.8,0.8,0.9,0.9,0.99,0.99,1.0 
${temp_trans} | tee ${temp_file}`;

My questions are:

1. Is this the correct way to apply the inverse transform? I get a weird 
result in that the mean native GM volume actually decreases with respect 
to that obtained from the original volumes in talairach space, but the 
mean native WM and CSF volumes increase. This is confusing, given that 
it is a linear transform, which I believe should deform in a globally 
proportional way.

2. Is there a better (more continuous) way to calculate volume than my 
step #3? The binning method essentially smooths the data, instead of 
simply summing the PVE values from all voxels.

Thanks!

-- 
Andrew Reid
Department of Cognitive Neuroscience
Radboud University Nijmegen Medical Centre
Postbus 9101, 6500 HB Nijmegen
The Netherlands

phone +31 24 3666171
web www.neuropi.org