NITRC: MRIcron: help

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help > No overlap between overlay and background - these images do not appear coregistered.

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No overlap between overlay and background - these images do not appear coregistered.

I am opening MRI scans in MRIcron, and the I am adding other nii.gz files over it as an overlay. But, it gives me an error message as mentioned in the Title. I'd like to know how I can add the overlay without getting this error.

RE: No overlap between overlay and background - these images do not appear coregistered.

Sounds like you have to register the two images to a common space. You can use SPM's coregister, FSL's FLIRT or AFNI's 3dWarpDrive

RE: No overlap between overlay and background - these images do not appear coregistered.

Thank You very much for the suggestions. I hope that these tools will fix the problem for me.

RE: No overlap between overlay and background - these images do not appear coregistered.

One more question.
Is it possible for T2 MR images to be converted to the MNI space? I have been using FSL-Flirt for it, but I think it converts onlt T1 images to the MNI space.

RE: No overlap between overlay and background - these images do not appear coregistered.

This question is out of scope for this forum. Consider posting on the fsl jiscmail support list. You should consider using a modality specific reference image or a cross-modal cost function.