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)
Hi,
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.
Cheers,
Julien
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.
Thanks!!