Slicer version: 4.8.1
I am aiming to automate spinal cord segmentation from MR images. I have been using Spinal Cord Toolbox (SCT); a Linux-based open-source software dedicated specifically to the processing and analysis of the spinal cord. The documentation of the Spinal Cord Toolbox module sct_propseg which I have been using is listed here: https://sourceforge.net/p/spinalcordtoolbox/wiki/sct_propseg/
I have been testing SCT’s automated segmentation through Slicer and it works for this MR image of the cervical vertebrae:
However, the issue I am experiencing is poorly automated spinal cord segmentation for my lumbar vertebrae images. In fact, SCT seems to fail to segment my T1 image. Even stranger, my T2 image (spinal cord = dark, CSF = bright) is being segmented poorly when selected as a T2 image but adequately when selected as a T1 image (spinal cord = bright, CSF = dark).
I believe that the lumbar vertebrae images are not being processed correctly due to the spinal cord not being well-defined as well as poor contrast between the spinal cord and the cerebrospinal fluid (CSF):
In fact, the recommendations listed here https://sourceforge.net/p/spinalcordtoolbox/wiki/correction_PropSeg/ suggest that the image should be edited to more clearly enhance these features. However, these editing procedures are complicated and my workflow would no longer consist of automated segmentation.
I have investigated equivalent Slicer semi-automated segmentation tools as an alternative and indeed, they work for the cervical vertebrae image. Some initialization (albeit very limited) is required by the user (which may impede its effectiveness); moreover, these tools do not perform as well as SCT but are satisfactory enough for my needs.
Unfortunately though, these tools are not adequate for the lumbar vertebrae images discussed above.
Thus, any suggestions on how I should proceed or advice concerning the appropriate tools or programs that can automate spinal cord segmentation would be greatly appreciated.