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config_radiomics_extraction.yaml
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config_radiomics_extraction.yaml
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# PROCESSING PARAM.S
proc:
# number of cores to use
cpu_cores: 8
# DATA INFORMATION
data:
#Top folder that contains the BMS project
base_path: '/Volumes/MYDRIVE/Maastro/Data/p0484-risk-ms-st3-nsclc/'
# preprocessed data folder - where all the converted nrrd files are stored
nrrd_base_path: '/Volumes/MYDRIVE/Maastro/Data/p0484-risk-ms-st3-nsclc/processed/nrrd/'
# name of the subfolder, under each patient folder, where the segmentation masks
# (inferred by the pipeline, resampled, converted to NRRD) are stored
pred_segmasks_folder_name: "rt_binarymasks"
# name of the ROIs from which the radiomic features will be extracted from
rois_to_input: ["GTV"]
# Excluded patients (for example missing files, ROIs)
#List of excluded patients without GTVp1
#excluded_patients: ["P0484C0006I13347712","P0484C0006I13348105","P0484C0006I13349751","P0484C0006I13352429","P0484C0006I13353173","P0484C0006I13358312","P0484C0006I13359183","P0484C0006I13362784","P0484C0006I13363429","P0484C0006I13364175","P0484C0006I13365895","P0484C0006I13366119","P0484C0006I13369845","P0484C0006I1902800","P0484C0006I3078632","P0484C0006I4221336","P0484C0006I5394488","P0484C0006I5822367","P0484C0006I59369","P0484C0006I6553728","P0484C0006I7903295","P0484C0006I8868250"]
#List of excluded patients without GTVnsum
#excluded_patients: ["P0484C0006I13347331","P0484C0006I13347539","P0484C0006I13349927","P0484C0006I13351656","P0484C0006I13352562","P0484C0006I13352595","P0484C0006I13352907","P0484C0006I13354939","P0484C0006I13354987","P0484C0006I13355627","P0484C0006I13356256","P0484C0006I13357020","P0484C0006I13357957","P0484C0006I13362687","P0484C0006I13365669","P0484C0006I13366348","P0484C0006I13366557","P0484C0006I13367199","P0484C0006I13367213","P0484C0006I13367610","P0484C0006I13368733","P0484C0006I13369197","P0484C0006I1464723","P0484C0006I18991","P0484C0006I400173","P0484C0006I4727106","P0484C0006I5877329","P0484C0006I6960259","P0484C0006I7964928","P0484C0006I8108763"]
excluded_patients: []
# extraction INFORMATION
radiomics:
# name of the config file that configures feature extraction
config_path: '/Users/albitraverso/WorkspaceMaastro/P0484_GTV_NSCLC/src/configs_radiomics_extraction_GTVNSCLC.yaml'
# name of base ouput folder where the radiomic features, for each patient and for each ROI will be stored
radiomics_out_path: '/Users/albitraverso/WorkspaceMaastro/P0484_GTV_NSCLC/analysis/'
# GENERAL DATASET INFORMATION
dataset:
# name of the dataset - can be used for logging purposes
name: 'GTVNSCLC_SNUH'