Reply To: Grey matter and white matter volumes 2523412.nii.gz


The hemi.label file is an intermediate file that we use to roughly identify regions of the brain. If you load the hemi.label.nii.gz file in brainsuite, you will see that it labels the right and left brainstem, cerebrum, and a general subcortical area.

You can take a look at your tissue classification results by opening the pvc.label.nii.gz or pvc.frac.nii.gz
Here’s a video where I explain the brainsuite outputs:

In order to get calculations of GM/WM/CSF and total volume, run your subject through SVReg which can be run on the GUI or command line. (instructions found here:
it will output a roi.stats.txt file which outputs volume measurements which you can open in excel. the 1st line will give you total CSF volume, 2nd: GM Vol and 3rd WM Vol.
It will also list regional measurements and you can find the description of the ROI IDs by opening the brainsuite_labeldescription.xml

It looks like for this subject I get
CSF: 272.569
GM: 682.809
GM+WM: 1204.774

BrainSuite uses partial volume tissue classification which considers that some voxels are composed of mixed tissue and assigns it that way. So a single voxel can be calculated as 40% GM and 60% WM which is why you get voxels labeled as GM/WM or GM/CSF. This can give you more accurate measurements.