Extracting metrics from lesion masks



I have binarised cervical cord lesion masks that I manually segmented and which are currently in t2 space. I also have cervical cord MTR and diffusion data (which I have already processed). I now would like to extract the mean MTR and mean FA/MD of the lesional tissue. Is there a way of doing this using SCT?

Thank you very much!



Hi Romina,

You can use sct_analyze_lesion, which takes as input the lesion mask, the cord segmentation and the metric of interest (e.g., MTR image) and which outputs a lesion mask with each lesion labeled (1, 2, 3, …) as well as an Excel file with the metrics for each lesion.

Here is an example, where I created a mask with three dummy squares on a T2w image:

Running this command:

sct_analyze_lesion -m t2_mask.nii.gz -i t2.nii.gz -s t2_seg.nii.gz

produces the labeled lesion mask:


and the associated metrics:



Hi Julien,

Great, thank you very much! Quick additional questions - if you have your t2 lesion mask and want to extract the mean MTR, which images would you input for each command and/or are there any additional registration steps that you need to run beforehand?

Many thanks!



You would need to co-register the T2 and the MTR, and then apply the transformation to the T2 lesion mask. So, something like this:

sct_register_multimodal -i T2 -d MTR
sct_apply_transfo -i T2_MASK -d MTR -w warp_T2toMTR
sct_analyze_lesion -i MTR -s MTR_seg -m T2_MASK_reg

Alternatively, you can work in the PAM50 space: register your T2 and MTR with the PAM50 template, apply the transformation of the lesion mask to the PAM50, and then extract metrics in the PAM50 space.