Registration between two segmentations (multimodal)

Dear SCT team,

I am looking to co-register a T2 structural MRI with a CT image. I have for both the labeled vertebrae segmentation. I would like to use the SCT’s sct_register_multimodal command to do so. I have been looking at different options but would very much appreciate if you have a suggestion.

Kind of T2 images:

Kind of CT images

Thank you in advance! (again)


If you have the labeled vertebrae you could (should) use label-based segmentations. I’m happy to optimize the syntax for you if you send me both labels.


Hi Julien!

Thank you so much for your fast response!

You can find them in this link.



Hi Sergio,

I came up with something that works reasonably well. Here’s the syntax:

sct_register_multimodal -i S1_T2.nii.gz -d S1_CT.nii.gz -ilabel S1_T2_labels.nii.gz -dlabel S1_CT_labels.nii.gz -iseg S1_T2_seg.nii.gz -dseg S1_CT_seg.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz_Rx_Ry_Rz:step=1,type=seg,algo=affine

Before registration:

After registration:

Now, I’ve only tried one combination of parameters (because the CT data is large, it is slow to run), but I encourage you to try tweaking step=1. A few things to try: change the shrink factor (to 2 or 4), increase the number of iterations, add smoothing. I wouldn’t play with non-affine transformations, because the information content between the CT and MRI vertebrae segmentation is quite different, so you would end up with non-robust results. While you do this optimization I encourage you to visualize the output of the step=1 (use the flag -r 0 to keep the intermediate results), as shown below (red: before step1, green: after step1, white: CT segmentation):


Hi Julien!

Thank you very much! I was indeed playing with a few things, but this is already better. I was missing step=0,type=label,dof=Tx_Ty_Tz_Rx_Ry_Rz.

I’ll update here the params as it goes.


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