Extract voxel mean intensity across ROIs

SCT
1

Hi experts,
I’m looking to compute the mean voxel intensity for quantitative imaging in the SC.
I’m planning on using sct_extract_metric and using it as though it were MTR with the MAP option.
I’ve registered the template to the input already - just wondering if sct_extract_metric is extracting the mean voxel intensity in this case?
Thanks!

2

Hi Thomas,

sct_extract_metric does indeed compute a “mean” value across voxels specified in the mask (e.g., spinal cord, white matter, or specific tract). The function works regardless what your input image is. It could be MTR, DTI-FA, or even a T2-weighted image.

Note that I put “mean” in quotation because strictly speaking, the MAP algorithm does not exactly compute the mean, but rather a value based on Gaussian mixture modelling (see the paper by Levy et al. in Neuroimage for more details).

3

Thanks @jcohenadad !
I’m calculating T1 and QSM values, so probably just the mean. I will use weighted mean instead of map :slight_smile:
Thanks again!