Hi,
Thanks for the response. Thresholding does not seem to be the issue though. I am using a T1 image to warp to standard space. I believe the issue is that my patient T1 scans have lesions, while the reference image does not and so the warp is correcting for the differences in intensities in those voxels by essentially shrinking them.
When I apply the transformation matrix I get from that process to my lesion masks, I'm guessing the same thing is happening.
Is there a way to mask out the lesions on the T1 images itself by reducing the intensity contrast so FNIRT does not try to remove them?
Thanks,
Calvin
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