Why do I loose labels when warping atlas in subject space?

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1

I want to warp AAL atlas on individual subject space. I am using Ants and so a code like this:

antsApplyTransforms -d 3 -e 3 -i /pathto/AAL3v1_2mm.nii.gz -r pathto/subj.nii.gz -o /pathto/$AAL3v1_2mm_on_subj.nii.gz $INV_transformation -n MultiLabel

The resulting transformed label has less labels than the original labeled image. How can it be possible?

2

The parcels that get lost are probably small enough that they get crowded out by other parcels in the resampling step.

On a related note, I think the ANTs folks recommend GenericLabel over MultiLabel for atlases.

3

Thank you very much. I will try!

4

Using GenericLabel, labels result to be shifted with respect to brain…

using -n GenericLabel
AALGenericLabel

I am not completely satisfied even with the MultiLabel result since, in this way, labels do not cover all Grey Matter brain.

5

Hi,

This poor alignment suggests a problem with the transforms. From your first post, I see you did

antsApplyTransforms -d 3 -e 3 -i /pathto/AAL3v1_2mm.nii.gz -r pathto/subj.nii.gz -o /pathto/$AAL3v1_2mm_on_subj.nii.gz $INV_transformation -n MultiLabel

what is the value of INV_transformation?

Also, pathto/subj.nii.gz needs to be a 3D image in this call. It can’t be a time series, for example.