Registration of MRI to CT for the Spine

Hi, sorry to bother you all again. I have to registered the T1 to T2 scans just fine using the Brainsfit Module, however with regards of T2 to CT scans I am having a bit of trouble.
I already used “Fudicial Registration” to get initial allignment for the registration, but when I attempt to use non-deformable registration it seems like the scans automatically get cropped. (This occurs in a multitued of the other registration phases as well) and the scans are not as alligned as I want them to be.

I was wondering if there are any resources for spine registration? Or what parameter needs to be changed so at least the entire scan is not cropped to a specific location in the spine.

Original:
image

After Registration:
image

Hi triple_axel,
Did you solve this problem with registration?
I´m having the same issue in version 4.11.0
authought I sucessfuly performed a landmark registration in ver 4.8
impossible to register with fiducials…
How do you aquire yor MRI images?
tks

You can use latest stable or preview release (currently 4.10 or 4.11). Do not use anything older.

Landmark registration always works (I would recommend Fiducial registration wizard module in SlicerIGT extension), but it requires some effort to place the points accurately.

Ifnyou segment vertebrae, then you can use Segment Registration extension to compute transforms based on that

Intensity-based automatic image registration (e.g., SlicerElastix) should work well, too, but you may need a reasonable initial alignment (less than 10mm and 10 deg error) and images need to be cropped to approximately the same anatomical region.

Probably the best is to combine methods: do initial approximate alignment using landmark registration, then crop the images to the region of interest and register using Elastix. If this works well then you can write a simple scripted module that automates these steps, so that you don’t need to click many times and switch between several volumes.