I am trying to align the MR, CT and PET files in CC Tumor Heterogenity dataset. But I am facing issues with the tags in coregistration files not matching with corresponding folders of MRI,CT,PET etc. Need help with the coregistration file details.
What have you tried so far? I’m not familiar with the collection, but from a quick look at the data it appears that the source data and registration objects are all available.
I tried uploading the co-registration file, along with the corresponding MR-CT and PET-CT folders in 3D Slicer to register the slices and save them. But, the PET-CT transformation matrix does not rotate the moving image. It merely moves the images closer. I tried volume rendering the same as well, but the volumes are not registering when using the given matrix in the co-reg files. (Although it did work for PET-MR).
To check for mapping among Coreg files, CTs and MRIs, I tried extracting the UIDs of files given in folders for patient A01. But I could not find matching series or instance IDs in the MR1-CT1 co-registration file that is within the same folder as MR1 and CT1. I wanted to know what could be possibly going wrong here, and if there is a better approach to this.
This is the post-alignment screenshot for Patient A01- PET1-CT1 :
I haven’t worked directly with this data, but the since you said it worked for PET-MR but not for PET-CT then it’s possible the datafiles themselves are not correct.
The fact that the CT is upside down in this image is a big red flag that something is incorrect in the data. Is that the way the CT loaded in Slicer or is that after applying the transform?
Are you using the SlicerRT extension to read the dicom registrations? Or how do you get them?
Yes, I am using SlicerRT, I am loading the volumes and then loading the Coregistration file as Dicom Import.
This is how PET and CT volumes render before applying the transform:
Not much difference evident, except for a slight shift towards each other.
Okay, to get to the bottom of thincs can you describe your exact steps and what software versions etc lead to what you observe?