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Updated readme to revert to prior version (to correct a push error) and added details on the lesion class file.
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Renato Cuocolo
2020-09-14 09:58:24 +02:00
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@@ -9,7 +9,9 @@ We encourage the use of this data for radiomics and machine learning investigati
## Files
The files are in compressed NIFTI (.nii.gz) format and collected in separate folders for T2 and ADC images. Each filename contains the following information (separated by underscores):
### Lesion masks
The files are in compressed NIFTI (.nii.gz) format and collected in separate folders for T2 and ADC images (n = 299 lesions). Each filename contains the following information (separated by underscores):
- "PROSTATEx Patient ID" + "Finding ID" + "Sequence name" + "ROI"
@@ -19,6 +21,29 @@ As sometimes multiple axial ADC/T2 image sequences are available for a patient,
The sequence number corresponds to the number at the beginning of the PROSTATEx dataset DICOM image folders for each patient.
Finally, the "PROSTATEx_classes.csv" file contains the ground truths for all lesions included in the dataset, obtained from the orignial PROSTATEx and PROSTATEx2 data. This file is structured as follows (separated by underscores):
- ID column = "PROSTATEx Patient ID" + "Finding ID"
- Clinically Significant column (i.e. Gleason Score > 3+3, Gleason Grade Group/ISUP score > 1) = "True"/"False"
- Gleason Grade Group/ISUP score column = "No Biopsy" or 1-5
Patients who were classified as PI-RADS score = 2 did not undergo biopsy and their lesions are always assumed to be not clinically significant.
Full exam DICOM files are retrievable through the Cancer Imaging Archive at: [https://wiki.cancerimagingarchive.net/display/Public/SPIE-AAPM-NCI+PROSTATEx+Challenges](https://wiki.cancerimagingarchive.net/display/Public/SPIE-AAPM-NCI+PROSTATEx+Challenges)
### Prostate and zonal anatomy masks
The files are in compressed NIFTI (.nii.gz) format, and all segmentations have been performed on axial T2 images (n = 204 exams). Each filename contains the following information (separated by underscores):
- "PROSTATEx Patient ID"
The masks included in the "mask_prostate" directory represent whole-gland masks (binarized). Those included in "mask_pz" and "mask_tz" are limited respectively to the peripheral and rest (transition zone, central zone, anterior stroma) of the gland, also binarized. The last directory "mas_pz_tz" contains both annotations, with peripheral zone voxels having a value of 2 and the remaining (transition zone, central zone, anterior stroma) a value of 1. The backgorund always has a value of 0.
As sometimes multiple axial T2 image sequences are available for a patient, the repository also includes a list in CSV format containing the correct images for each mask. The list is structured as follows (separated by underscores):
- "PROSTATEx Patient ID" + "Sequence name" + "Sequence number"
The sequence number corresponds to the number at the beginning of the PROSTATEx dataset DICOM image folders for each patient.
Full exam DICOM files are retrievable through the Cancer Imaging Archive at: [https://wiki.cancerimagingarchive.net/display/Public/SPIE-AAPM-NCI+PROSTATEx+Challenges](https://wiki.cancerimagingarchive.net/display/Public/SPIE-AAPM-NCI+PROSTATEx+Challenges)
## License