Scan pre-processing
#1
by
JoHof
- opened
Hi Pillar-0 team,
first of all, congratulations on the great work you have done with this model and the paper! Could you please clarify how the pre-processing of ChestCT volumes should look like for inference of this model? Specifically:
- Should a 256^3 center crop be performed (should this be done on the original resolution or should be volume be downsampled?)
- Should the volume be resampled to an isotropic resolution before the center crop or any other fixed spacing?
Could you please provide a code snipped that shows all the steps one should perform for pre-processing a CT scan before inference?
In addition, I would be interested on the decision to perform a 256^3 center crop as opposed to a larger matrix like you did on the abdominal scans with 384?
Thanks a lot!
Thank you!
We preprocess our images using this repository: https://github.com/YalaLab/rave, which accepts both DICOM directories and NIfTI files.
- The volume is sampled to [1.25, 1.25, 1.25], then cropped or padded to 256x256x256. This is specified in our config for Chest CTs: https://github.com/YalaLab/rave/blob/main/configs/ct_chest.yaml.
- We determined the pixel spacing and final dimensions based on our data distribution at UCSF. The abdomen/pelvis scans had a greater field of view than the chest scans.
Hope this helps, please let us know if you have more questions!
yala
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