Running the Application

Note the ${fets_root_dir} from Setup.

Table of Contents

• Running the Application
  • Table of Contents
  • Application Path
  • Inference
    • Inference using BraTS-winning algorithms
    • Inference using the FeTS Consensus Models
  • Manual Corrections
  • Sanity Check
    • Phase-2 Intensity Check
  • Training
    • Ensure Sanity Checking Is Done
    • Transfer Certificates
    • Start Training

Application Path

cd ${download_location}
${fets_root_dir}/bin/FeTS # launches application

Please add the following path to your LD_LIBRARY_PATH when using FeTS: ${fets_root_dir}/lib:

export LD_LIBRARY_PATH=${fets_root_dir}/lib:$LD_LIBRARY_PATH

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Inference

Inference using BraTS-winning algorithms

${fets_root_dir}/bin/FeTS_CLI_Segment -d /path/to/output/DataForFeTS \ # data directory after invoking ${fets_root_dir}/bin/PrepareDataset
  -a deepMedic,nnunet,deepscan,fets_singlet,fets_triplet \ # all pre-trained models currently available in FeTS see notes below for more details
  -lF STAPLE,ITKVoting,SIMPLE,MajorityVoting \ # if a single architecture is used, this parameter is ignored
  -g 1 \ # '0': cpu, '1': request gpu
  -t 0 # '0': inference mode, '1': training mode

The aforementioned command will perform the following steps:

• Perform inference on the prepared dataset based on selected architectures and label fusion strategies
  • NOTES:
    • nnUNet should have been downloaded during the installation process. In case there was a failure, follow these steps:
      • Download weights from this URL or from the command line:

        cd ${fets_root_dir}/data/fets
        wget https://upenn.box.com/shared/static/f7zt19d08c545qt3tcaeg7b37z6qafum.zip -O nnunet.zip
        unzip nnunet.zip
        

      • Unzip it in ${fets_root_dir}/data/fets. The directory structure should look like this:

        ${fets_root_dir}
        │
        └───data 
        │   │
        │   └──fets
        │   │   │
        │   │   └───nnunet
        │   │   │   │
        │   │   │   └───${training_strategy}.1_bs5 # the specific training strategy
        │   │   │   │   │
        │   │   │   │   └───fold_${k} # different folds
        │   │   │   │   │   │ ...
        

      • This will now be available as a model for inference using the FeTS_CLI_Segment applications under the -a parameter.
    • To run DeepScan, at least 120G of RAM is needed.
    • DeepMedic runs as a CPU-only task.
• Leverage the GPU
• Place inference results on a per-subject basis for quality-control:

  DataForFeTS
  │
  └───Patient_001 # this is constructed from the ${PatientID} header of CSV
  │   │ Patient_001_brain_t1.nii.gz
  │   │ Patient_001_brain_t1ce.nii.gz
  │   │ Patient_001_brain_t2.nii.gz
  │   │ Patient_001_brain_flair.nii.gz
  │   │
  │   └──SegmentationsForQC
  │   │   │ Patient_001_deepmedic_seg.nii.gz # individual architecture results
  │   │   │ Patient_001_nnunet_seg.nii.gz
  │   │   │ Patient_001_deepscan_seg.nii.gz
  │   │   │ Patient_001_fused_staple_seg.nii.gz # label fusions using different methods
  │   │   │ Patient_001_fused_simple_seg.nii.gz
  │   │   │ Patient_001_fused_itkvoting_seg.nii.gz
  │
  └───Pat_JohnDoe
  │   │ ...
  

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Inference using the FeTS Consensus Models

${fets_root_dir}/bin/FeTS_CLI_Segment -d /path/to/output/DataForFeTS \ # data directory after invoking ${fets_root_dir}/bin/PrepareDataset
  -a fets_singlet,fets_triplet \ # can be used with all pre-trained models currently available in FeTS
  -lF STAPLE,ITKVoting,SIMPLE,MajorityVoting \ # if a single architecture is used, this parameter is ignored
  -g 1 \ # '0': cpu, '1': request gpu
  -t 0 # '0': inference mode, '1': training mode

The aforementioned command will run inference using the FeTS Consensus models (both singlet and triplet) for the data directory specified by -d. The output will be placed in the directory specified by -o.

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Manual Corrections

• Use the FeTS graphical interface (or your preferred GUI annotation tool such as ITK-SNAP or 3D-Slicer) to load each subject’s images:

  

• And each segmentation (either individual architectures or the fusions) separately:

  

• Perform quality control and appropriate manual corrections for each tumor region using the annotation tools:

  

  • Ensure BraTS annotation protocol is followed for labels:

  Label	Region	Acronym
  1	Necrotic Core of Tumor	NET
  2	Peritumoral Edematous & Infiltrated Tissue	ED
  4	Enhancing/Active part of tumor	ET

• Save the final tumor segmentation as ${SubjectID}_final_seg.nii.gz under the subject’s directory:

  DataForFeTS
  │
  └───Patient_001 # this is constructed from the ${PatientID} header of CSV
  │   │ Patient_001_brain_t1.nii.gz
  │   │ Patient_001_brain_t1ce.nii.gz
  │   │ Patient_001_brain_t2.nii.gz
  │   │ Patient_001_brain_flair.nii.gz
  │   │ Patient_001_final_seg.nii.gz # NOTE: training will not work if this is absent!!!
  │
  └───Pat_JohnDoe
  │   │ ...
  

  • NOTES:
    • This file is is used during training and the subject will be skipped if this is absent
    • A video example is here: https://www.dropbox.com/s/6p62ztqf7ckoial/FeTS_refinements_tutorial.mp4?dl=0

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Sanity Check

Before starting final training, please run the following command to ensure the input dataset is as expected:

cd ${fets_root_dir}/bin
./OpenFederatedLearning/venv/bin/python ./SanityCheck.py \
  -inputDir /path/to/output/DataForFeTS \
  -outputFile /path/to/output/sanity_output.csv

Note: If you are running FeTS version 0.0.2 (you can check version using FeTS_CLI --version), please do the following to get the SanityChecker for your installation:

cd ${fets_root_dir}/bin
wget https://raw.githubusercontent.com/FETS-AI/Front-End/master/src/applications/SanityCheck.py

Phase-2 Intensity Check

During discussions with some of the collaborating sites, we note negative values randomly coming up in the pre-processed scans. To identify these cases, we have now put together an additional script to assess all pre-processed images for the negative values and provide relevant statistics. This can be run in the following manner:

cd ${fets_root_dir}/bin
wget https://raw.githubusercontent.com/FETS-AI/Front-End/master/src/applications/Phase2_IntensityCheck.py
./OpenFederatedLearning/venv/bin/python ./Phase2_IntensityCheck.py \
  -inputDir /path/to/output/DataForFeTS \
  -outputFile /path/to/output/intensity_check.csv

If /path/to/output/intensity_check.csv doesn’t get generated, that means the dataset is completely fine, otherwise, please send the file to admin@fets.ai for debugging.

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Training

Ensure Sanity Checking Is Done

Proceed to training once sanity check (↑) is successfully finished.

Transfer Certificates

If you have a signed certificate from a previous installation, ensure they are copied before trying to train:

cd ${fets_root_dir}/bin/
cp -r ${fets_root_dir_old}/bin/OpenFederatedLearning/bin/federations/pki/client ./OpenFederatedLearning/bin/federations/pki

Start Training

${fets_root_dir}/bin/FeTS_CLI -d /path/to/output/DataForFeTS \ # input data, ensure "final_seg" is present for each subject
  -c ${collaborator_common_name} \ # common collaborator name created during setup
  -g 1 -t 1 # request gpu and enable training mode

The aforementioned command will perform the following steps:

• Train a model with a 3DResUNet architecture (more architectures will be made available in future releases) for all the complete subjects (i.e., with ${SubjectID}_final_seg.nii.gz and all 4 structural modalities present) in a collaborative manner
• Leverage the GPU
• Perform full-image validation during training

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Next: Contact FeTS Admin