Coregister lesion mask to T1

Hi experts,

I have a lesion mask that has been created from T1 with a lesion. They are exactly the same but they are in different spaces. I want to register the lesion mask to the T1 but it shows mismatching.

I tried using SPM, flirt and mrtransform
mrtransform lesion.nii output.nii -template T1.nii

Non of them has done the job.!

  • Despite all this, HOW can I register a lesion mask to T1, if they are exactly the same but in different spaces?


Hi Salah,

From which image was the lesion mask created? You would need to register that image to your T1 and apply the resulting transformation on your lesion mask. Directly registering the mask to your T1 will not work (as you noticed) as both images do not have sufficient similarities.


Hi Salah,

There might be a terminology problem here; please see this wiki page. In particular if you have generated the lesion mask from the T1w image, there should be no reason to register that image to the T1w. What I’m hypothesizing might be going on is that you’ve generated the lesion mask from the T1w image before a transformation was applied to the latter, and so now you have an issue where the content of the two images do not overlap. But what you want to do is take the transformation that was applied to the T1w, and also apply it to the lesion mask. This does not involve “image registration”.

I would also note that you mrtransform call is not actually applying any spatial transformation; it is only resampling the data from lesion.nii onto the voxel grid as defined by template image T1.nii.


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