Preparing the configuration file for running MRI_GBM_Postop_FV_5p model in Colab Notebook about raidionics

[dbouget]

Hi @gusSCIMOV,
I've added a new notebook regarding how to run the postoperative GBM segmentation model, and a second notebook including the postoperative reporting step.

Don't hesitate to re-open this issue if you need additional help!

[gusSCIMOV]

Oh thank you so much for your timely and quick reply. Works pretty good with the Pre-op Post-op pair.
Just a more specific question about it:
Even though we should include the pre-surgical tumor burden to get better estimation of the post-surgery, I'm dealing with a mix of MRI where Pre-operative scans are not always available. In those cases, may I comment and skip the steps involving Pre-op MRI and only use the 4 Post-op modalities? For example; going over and just commenting the full blocks related with "Registration from T1-CE (T0) to T1-CE (T1) or the input[3] and input[4] as well (timestamp 0)

pipeline_json[step_str]["fixed"]["sequence"] = "T1-CE"
pipeline_json[step_str]["description"] = "Registration from T1-CE (T0) to T1-CE (T1)"

pipeline_json[step_str]["inputs"]["3"] = {}
pipeline_json[step_str]["inputs"]["3"]["timestamp"] = 0
pipeline_json[step_str]["inputs"]["3"]["sequence"] = "T1-CE"
pipeline_json[step_str]["inputs"]["3"]["labels"] = None
pipeline_json[step_str]["inputs"]["3"]["space"] = {}
pipeline_json[step_str]["inputs"]["3"]["space"]["timestamp"] = 1
pipeline_json[step_str]["inputs"]["3"]["space"]["sequence"] = "T1-CE"
pipeline_json[step_str]["inputs"]["4"] = {}
pipeline_json[step_str]["inputs"]["4"]["timestamp"] = 0
pipeline_json[step_str]["inputs"]["4"]["sequence"] = "T1-CE"
pipeline_json[step_str]["inputs"]["4"]["labels"] = "Tumor"
pipeline_json[step_str]["inputs"]["4"]["space"] = {}
pipeline_json[step_str]["inputs"]["4"]["space"]["timestamp"] = 1
pipeline_json[step_str]["inputs"]["4"]["space"]["sequence"] = "T1-CE"

Thanks
GP

[dbouget]

I've updated the README to the Raidionics model zoo. There are 5 different postop glioblastoma segmentation models, each trained for a specific set of inputs.

If you need to run a model on postop MR scans only, you can look at the following models: MRI_GBM_Postop_FV_1p, MRI_GBM_Postop_FV_2p, and MRI_GBM_Postop_FV_3p. There is a pipeline.json file inside each model folder, where you can copy the actual pipeline required for running the segmentation with the specific model.