I am running a radiomics project that requires segmentation/mask of medical imaging files. The simplest example is that MRI scans are rigidly registered to a CT scan and contours/segments applied.
The contours/segments are referenced to the CT scan at default and not the MRI. What I want is to resample the MRIs such that if the segments are loaded with the MRI that they align with the MRI.
In the DICOM header file for the registration file between the MR and CT there is a DICOM tag “FrameOfReferenceTransformationMatrix” which stores the information of the rigid registration of the MR to the CT. This consists of a list of 16 numbers ending with 0 0 0 1.
I’ve plugged in the numbers into a ITK file as follows
#Insight Transform File V1.0 #Transform 0 Transform: TranslationTransform_double_3_3 Parameters: 1 0 0 0 0 1 0 0 0 0 1 0 FixedParameters: 0 0 0
However the transform that is applied does not work in the way I want it to. The image IS resampled but it is not aligning to the same reference point as the CT. I’ve rearranged the matrix numbers but this doesn’t seem to help the problem. The only way to get alignment is to manually put in numbers.