This application provides an estimate of the pseudo-progression after radiotherapy in glioblastoma patients, via multi-parametric MRI analysis, as shown in [1].
REQUIREMENTS:
- Co-registered Multimodal MRI: T1, T1-Gd, T2, T2-FLAIR, DSC-MRI, DTI-AX, DTI-FA, DTI-RAD, DTI-TR. Ensure that these are the identified modalities in the drop-down menus next to each loaded image.
- Segmentation label of the demarcated region of interest (Label=1) in a single NIfTI (.nii.gz) file.
- The data for each patient should be organized in the following directory structure.
- SubjectID
- CONVENTIONAL
- "my_T1_file.nii.gz"
- "my_T2_file.nii.gz"
- "my_T1CE_file.nii.gz"
- "my_FLAIR_file.nii.gz"
- DTI
- "my_AX_file.nii.gz"
- "my_FA_file.nii.gz"
- "my_RAD_file.nii.gz"
- "my_TR_file.nii.gz"
- PERFUSION
- "my_PERFUSION_file.nii.gz"
- SEGMENTATION
- "my_segmentation_file.nii.gz"
- The data of multiple patients should be organized in the above mentioned structure and reside under the same folder, e.g.:
- Data_of_multiple_patients
- Subject_ID1
- Subject_ID2
- ...
- Subject_IDn
USAGE:
- Pseudoprogression assessment on a batch of subjects.
- "Train a new model":
- Select the "Training Directory", e.g., Data_of_multiple_patients (confirm the data follows the structure instructed above).
- Select the "Output Directory" where the trained model should be saved.
- Click on 'Confirm'.
- A pop-up window will confirm the completion of model training (~1.5*NoOfSubjects minutes).
- This application is also available as with a stand-alone CLI for data analysts to build pipelines around.
- NOTE: in the sample data, we are providing multiple duplicates of 5 unique subjects to show the training functionality at work; the model generated using these should NOT be used to generate results.
PseudoProgressionEstimator.exe -t 0 -i C:/PseudoprogressionSubjects -o C:/PseudoprogressionModel
- "Use existing model":
- Select the "Model Directory". Note that a model trained on a cohort of HUP can be found in ftp://www.nitrc.org/home/groups/captk/downloads/models/pseudoprogression.zip
- Select the "Test Directory", e.g., Data_of_multiple_patients (confirm the data follows the structure instructed above).
- Select the "Output Directory", where the user wants to save the infiltration maps.
- Click on 'Confirm'.
- A pop-up window will confirm the completion of assessment of pseudoprogression (~1.5*NoOfSubjects minutes).
- This application is also available as with a stand-alone CLI for data analysts to build pipelines around:
PseudoProgressionEstimator.exe -t 1 -i C:/PseudoprogressionSubjects -o C:/PseudoprogressionOutput -m C:/PseudoprogressionModel
RESULT INTERPRETATION:
- 1st column: distance to hyperplane that classifies pseudo-progression versus the rest
- 2nd column: distance to hyperplane that classifies true-progression versus the rest
Reference:
-
H.Akbari, S.Bakas, M.Martinez-Lage, M.Nasrallah, M.Rozycki, S.Rathore, G.Shukla, S.Mohan, M.Bilello, C.Davatzikos, "Quantitative radiomics and machine learning to distinguish true progression from pseudoprogression in patients with GBM", ASNR 56th Annual Meeting, 2018.