Understanding sct_register_multimodal output


I am currently using SCT 5.3.0 version and I am trying to register 2D T2* image to MT-ON image. Here is command that I am using:

sct_register_multimodal -i 2D_T2_STAR.nii.gz -d MT_ON.nii.gz -iseg 2D_T2_STAR_SEG.nii.gz -dseg MT_ON_SEG.nii.gz -m 2D_T2_STAR_MASK.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,algo=syn,slicewise=1,iter=1,metric=CC -ofolder .

As the result I get following images:

2D_T2_STAR_reg.nii.gz, MT_ON_reg.nii.gz, warp_2D_T2_STARMT_ON.nii.gz, warp_MT_ON2D_T2_STAR..nii.gz

What I fail to understand is whether or not sct_register_multimodal is registering images in the same MID space, so I have to use 2D_T2_STAR_reg.nii.gz and MT_ON_reg.nii.gz, or does it register in both ways so I have to use 2D_T2_STAR_reg.nii.gz and ORIGINAL MT_ON.nii.gz? In which space are the resulting images?

Also, if you have any suggestions on parameters I should pass for better accuracy I would appreciate it, thanks!

Hi @StefanCepa995,

There is no mid-space. Here are the descriptions of each file:

  • 2D_T2_STAR_reg.nii.gz: 2D_T2_STAR.nii.gz registered to the MT_ON.nii.gz space
  • MT_ON_reg.nii.gz: MT_ON.nii.gz registered to the 2D_T2_STAR.nii.gz space
  • warp_2D_T2_STAR2MT_ON.nii.gz : Warping field (forward) that brings 2D_T2_STAR.nii.gz to MT_ON.nii.gz
  • warp_MT_ON2D_T2_STAR.nii.gz : Warping field (backward) that brings MT_ON.nii.gz to 2D_T2_STAR.nii.gz

I hope that helps!

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Hi @jcohenadad

Thanks for clarification and sorry for late response!

This has helped me a lot!

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