CSV File

In MEDimage every dataset must have a csv file along with it, this file contains information about the scans in the dataset that will be used in the radiomics analysis, especially ROI names used each scan. Since scans can have multiple ROIs, the user need to specify for each scan tha ROI name(s) to use for the processing and radiomics extraction. The csv files are also used by the DataManager in pre-checks and summary creation (after raw data processing). The different columns of the file are:

  • PatientID: The scan patient ID, for example: "Glioma-TCGA-001".

  • ImagingScanName: Type of the imaging modality, usually "CT" for CT scans, "CT" for PET scans and MRI sequence for MR scans ("T1", "T2"…).

  • ImagingModality: Imaging modality ("CTscan", "MRscan" or "PTscan").

  • ROIname: ROI name for the analysis. Either addition or subtraction of ROIs or just a single ROI. Every ROI is put between brackets then added or subtracted to other ROIs. For example: "{swelling}+{edema}".

Note

The csv files must respect the following naming norm: "roiNames_{roi_label}.csv". For example: "roiNames_GTV.csv" for gross tumor volume. So different patients might have different ROI names, but the same roi label.

The following table is an example of a csv for a dataset of Soft-Tissue-Sarcoma (STS) cancer of 3 scans with different modalities (MR, CT and PET) and ROIs (GTV mass and GTV edema):

roiNames_GTV.csv

PatientID

ImagingScanName

ImagingModality

ROIname

STS-McGill-001

T1

MRscan

{GTV_Mass}+{GTV_Edema}

STS-McGill-001

T2

MRscan

{GTV_Edema}-{GTV_Mass}

STS-McGill-002

CT

CTscan

{GTV_Edema}

STS-McGill-003

PET

PTscan

{GTV_Mass}

Note

Future works of MEDimage will aim to automate the creation of these csv files for each dataset and to implement ROIs intersection as well.