[MINC-users] Estimating tissue volume from PVEs
Andrew Reid
A.T.Reid at science.ru.nl
Tue Sep 2 11:20:49 EDT 2008
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
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