"Please explain how to extract MTR values for white matter and gray matter."

SCT
1

Dear SCT Team:
“Could you please explain how to extract MTR values for white matter and gray matter from mtr.nii.gz using t2s_gmseg.nii.gz and t2s_wmseg.nii.gz?
Additionally, could you explain how to add t2s_gmseg.nii.gz and t2s_wmseg.nii.gz to $SCT_DIR/data/PAM50/template/info_label.txt?”

2

Hi @ryu,

with sct_extract_metric you can either:

  • specify a mask to extract the metric from. Example: sct_extract_metric -i mtr.nii.gz -f t2s_gmseg.nii.gz, or
  • register the PAM50 template to the MTR data using the GM and WM contour from the T2*w scan, as explained here.

Additionally, could you explain how to add t2s_gmseg.nii.gz and t2s_wmseg.nii.gz to $SCT_DIR/data/PAM50/template/info_label.txt ?”

This cannot (and should not) be done, because the file info_label.txt refers to the PAM50 masks that are all co-registered to the PAM50 template (eg: PAM50_t2.nii.gz). More details in the SCT course.

3

Thank you very much!