About displaying MNI atlas on patient head MRI

Hi I’m new to use slicer. Can someone point me a bit on how to display the atlases (eg. MNI 2009 atlas or others used by Lead DBS) on patient space MRI images? I tried by dragging the atlas onto slicer, but the center is not aligned, or its’ not in correct location.

I tried to google for methods but did not find clear explanation. If I have run Lead DBS normalization beforehand, is it possible to use the results? Thanks for any suggestions.

Hi Lin, you can import the Lead-DBS normalization results as transforms in Slicer. You can use the inverse transform (MNI to patient) to transform the atlas models into patient space.


(post deleted by author)

Hi, the glanatComposite is the transform. There should also be a glanatInverseComposite (weird - perhaps an error from lead).

You can use the glanatComposite, import it as transform in Slicer, and invert it in the transforms module. Then apply it to the models.


Thanks a lot, man. I’ll take a try and get back to you soon.

(post deleted by author)

The normalization transforms from lead use the anat_t*.nii as reference.

If you center the volumes in slicer, you should take into account this transform.

I’d recommend to keep track of the transforms you apply to the images and you can use the transforms hierarchies in slicer to apply transforms to transforms, and so on.

You could also register the anat_t* from lead folder to your centered volume. And then use the resulting transform together with the glanat composite. This is probably easier.

This is a bit complex, and requires some knowledge of how images are represented in space, and how slicer manages this. I’d recommend to look a bit into this.

1 Like

Hi Simon, thanks for providing the two methods. I tried both but only did it correctly with the second way.
I’ll keep on trying.
Many thanks.

Hi Simon, I’ve aligned the atlas, with your help.
Now I need to do with the Warp module. Can you please tell me a bit about how to use it?
See the pic attached, what should I use as displacement field? Do I need to create one? I used Elastix to register anat_t1 with T1 image in slicer, but didn’t get grid transforms. Can you give me some clue on how to proceed? Thanks a lot.

You’d generally use the normalization output. Or any non linear transform you want to modify.

See SlicerNetstim/WarpDrive at master · netstim/SlicerNetstim · GitHub and WarpDrive - Lead-DBS User Guide for some more info. Still working on warpdrive to make it more user friendly.

1 Like