Aligning Segmentation and CT slices for feature extraction via Pyradiomics

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@Nav_Malhotra thank you for reaching out to ask about this in the forum!

pyradiomics, as many other tools, is designed to work more reliably with the data converted to one of the 3d research formats, such as NRRD or NIfTI. IDC data is stored in DICOM. Fortunately, conversion from DICOM to those research format is quite straightforward. I recommend the following:

  1. for DICOM CT series, you can use dcm2niix command line converter - you can install binary for your platform from the releases page here: Releases · rordenlab/dcm2niix · GitHub. Once you installed it, run dcm2niix pointing it to the directory containing a single CT series.
  2. for DICOM SEG series (I see from the identifier 9629abf6-d1de-4931-bc6a-061890ae275c in your screenshot that you were looking at the TotalSegmentator segmentations collection in IDC), you can use dcmqi segimage2itkimage tool for conversion (again, you can download binaries of dcmqi in the repo: Releases · QIICR/dcmqi · GitHub).

Can you tell me how you are downloading the files from IDC? We recently added some convenience functions to the idc-index that aim to simplify the process. You can learn about this from the updated download instructions page. Would be very interested to hear your thoughts and any feedback on this new functionality!

Hope this helps, but do let us know if you need more assistance!