Hi,
I would like to extract the amount of WM, GM and CSF from a hippocampal ROI.
I have a T2 rat brain acquired at 0.160 x 0.160 x 0.320 (TE 55). I multiply
the voxel size by 6 to get to 0.960 x 0.960 x 1.920 (otherwise I can't do
anything with the data in FSL because voxels are too small).
I follow the standard analysis protocol: Bet, estimate bias field + bias
field correction, and FAST on corrected volume. After FAST I get rest1 I get
the pve files for each tissue (prest1_pve_1=GM, rest1_pve_2=WM and
rest1_pve_0=CSF) and the seg files (rest1_seg_1, rest1_seg_2 and
rest1_seg_0) and the the whole brain segmented image rest1_seg. (rest1 is
the name of the volulme). I create a hippocampus mask called hippo-mask
(intensity 1) and use fslstats to extract the info for GM:
fslstats rest1_pve_1 -l 1 -u 1 -k hippo-mask -m
0.913644
fslstats rest1_pve_1 -l 1 -u 1 -k hippo-mask -v
6873 12161.580241
I do the same for WM rest1_pve_2 (l=2 and u=2) and for CSF rest1_pve_0 (l=0,
u=0).
I multiply the mean value (0.913644) with the 6873 to get the volume in
voxels - 6,279 - or multiply the mean value 6873 with 12161.580241 to get
the volume in cubic mm - 11,103. The values seem a little bit unusual to me
for a small rat hippocampus.
I would like to extract WM, GM and CSF from the hipopcampus and whole brain
volume to put them into a volumetric analysis.
I would be greateful for any suggestion on how to deal with this data or any
alternatives for the volumetric measurement.
Tamara
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