sbandred/mu-glioma-post-processed

Processed MU-Glioma-Post

Start Here

• —Use manifests/experiment_index.csv as the main case-level table.
• —Use manifests/longitudinal_index.csv when ordering patient timepoints for longitudinal work.
• —Use manifests/validation_summary.json to confirm the processed tree is complete.

Directory Guide

• —images_native/
• —Canonical modality symlinks to the source images.
• —File names use t1, t1c, flair, and t2.
• —images_reoriented/
• —Not populated because audit showed all volumes are already LPS.
• —images_resampled/
• —Not populated because audit showed all volumes are already 1.0 x 1.0 x 1.0 mm.
• —images_normalized/
• —Full-volume normalized images.
• —These are the default inputs for full-volume baselines.
• —masks/
• —Multi-class source-mask symlinks plus derived binary whole-tumor masks.
• —roi_tumor/
• —Tumor-centered ROI crops with a 16-voxel margin.
• —radiomics_inputs/
• —ROI-centered links intended for compact radiomics or ROI-based baselines.
• —manifests/
• —Process, validation, and merged cohort tables.

Key Files

• —manifests/experiment_index.csv
• —Merged split, processed-path, clinical, and label-volume table.
• —manifests/case_manifest.csv
• —Processing status per patient/timepoint.
• —manifests/mask_manifest.csv
• —Mask paths and mask-level processing details.
• —manifests/preprocessing_config.json
• —Frozen preprocessing parameters.

Clinical Timing Caveats

• —manifests/clinical_alignment_report.csv lists patient-level mismatches between imaging timepoint counts and the clinical workbook MRI-day columns.
• —The following imaging cases are missing days_from_diagnosis_to_mri in the current clinical workbook:
• —PatientID_0007 / Timepoint_3
• —PatientID_0220 / Timepoint_6
• —PatientID_0258 / Timepoint_1

Hugging Face

Upload this processed tree with:

python scripts/upload_processed_data.py --dataset-root processed

The uploader excludes local .cache/** and *.metadata files by default and automatically uses the large-folder upload path for large trees.