Processing the Data for FeTS

Data Requirements

• Brain MRI scans obtained from any manufacturer/model/field strength of scanner.
• Confirmed initial diagnosis of glioblastoma.
• Longitudinal patient assessments (3 or more post-op MRIs preferred per patient).
• Minimum suggested cohort of 40 patients (120 scans total).
• Required modalities per time-point (each preferably with axial or full 3D scan):
  • T1-weighted pre-contrast (T1): pre-contrast
  • T1-weighted post-contrast (T1Gd): Gd post-contrast
  • T2-weighted (T2)
  • T2 Fluid Attenuated Inversion Recovery (T2-FLAIR)

Data Arrangement

Each subject’s DICOM (or NIfTI) image is to be put in a separate folder:

Input_Data
│
└───Patient_001
│   │
│   └───Timepoint_001
│   │   │
│   │   └───T1
│   │   │   │ image_001.dcm
│   │   │   │ image_002.dcm
│   │   │   │ ...
│   │   └───T1GD
│   │   │   │ image_001.dcm
│   │   │   │ image_002.dcm
│   │   │   │ ...
│   │   └───T2
│   │   │   │ image_001.dcm
│   │   │   │ image_002.dcm
│   │   │   │ ...
│   │   └───T2FLAIR
│   │   │   │ image_001.dcm
│   │   │   │ image_002.dcm
│   │   │   │ .....
│   │
│   └───Timepoint_002
│   │   │
│   │   └───T1
│   │   │   │ image_001.dcm
│   │   │   │ image_002.dcm
│   │   │   │ ...
│   │   └───T1GD
│   │   │   │ image_001.dcm
│   │   │   │ image_002.dcm
│   │   │   │ ...
│   │   └───T2
│   │   │   │ image_001.dcm
│   │   │   │ image_002.dcm
│   │   │   │ ...
│   │   └───T2FLAIR
│   │   │   │ image_001.dcm
│   │   │   │ image_002.dcm
│   │   │   │ .....
│   │
│   └───Timepoint_N
│   
└───Patient_JohnDoe
│   │
│   └───Timepoint_001
│   │ ...   
│   │
│   └───Timepoint_002
│   │ ...   
│   
│ ...   
│   
└───Patient_SmithJoe
│   │ ...

• Ensure that unexpected “special” string characters that could hamper the file system’s processing are not present (read this article for more details). Some examples of this include (and are not limited to): !, @, #, $, %, ^, &, *, ', ;, :, ,, ~
• Please note that subject IDs should be unique strings and can be parsed by code. Some examples of problematic and acceptable subject IDs are as follows:
  • Problematic: “Patient_1”, “Patient_2”, …, “Patient_10”, …,”Patient_20”, …,”Patient_100”
  • Acceptable: “Patient_001”, “Patient_002”, …, “Patient_010”, …, “Patient_020”, …, “Patient_100”, …

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