Home

Documentation

GitHub

AssemblyNetDocker brick

3D Whole Brain MRI Segmentation using AssemblyNet (volBrain)

This brick allows to run the AssemblyNet Docker image.

Based on a large ensemble of convolution neural networks, AssemblyNet segment a T1w image in 133 labels (according to BrainColor protocol).

If you use this brick:

- cite: Pierrick Coupé, Boris Mansencal, Michaël Clément, Rémi Giraud, Baudouin Denis de Senneville, Vinh-Thong Ta, Vincent Lepetit, José V. Manjon AssemblyNet: A large ensemble of CNNs for 3D whole brain MRI segmentation. NeuroImage, Elsevier, 2020, 219, pp.117026.

- check the AssemblyNet’s license

This brick requires Docker

---

Mandatory inputs parameters:

• in_file (a string representing an existing file)

  Input T1w image (valid extensions: [.nii, .nii.gz]).

  ex. '/home/username/data/raw_data/T1w.nii'
  

Outputs parameters:

• native_t1 (a pathlike object or string representing a file)

  Filtered and normalized T1 image in native space.

  ex. '/home/username/data/derived_data/native_t1_T1w.nii.gz'
  

• mni_t1 (a pathlike object or string representing a file)

  Filtered and normalized T1 image in MNI space.

  ex. '/home/username/data/derived_data/mni_t1_T1w.nii.gz'
  

• native_mask (a pathlike object or string representing a file)

  Intracranial Cavity mask image in native space.

  ex. '/home/username/data/derived_data/native_mask_T1w.nii.gz'
  

• mni_mask (a pathlike object or string representing a file)

  Intracranial Cavity mask image in MNI space.

  ex. '/home/username/data/derived_data/mni_masks_T1w.nii.gz'
  

• native_structures (a pathlike object or string representing a file)

  Structures segmentation in native space.

  ex. '/home/username/data/derived_data/native_structures_T1w.nii.gz'
  

• mni_structures (a pathlike object or string representing a file)

  Structures segmentation in MNI space.

  ex. '/home/username/data/derived_data/mni_structures_T1w.nii.gz'
  

• native_macrostructures (a pathlike object or string representing a file)

  Macrostructures segmentation in native space.

  ex. '/home/username/data/derived_data/native_macrostructures_T1w.nii.gz'
  

• mni_macrostructures (a pathlike object or string representing a file)

  Macrostructures segmentation in MNI space.

  ex. '/home/username/data/derived_data/mni_macrostructures_T1w.nii.gz'
  

• native_lobes (a pathlike object or string representing a file)

  Lobes segmentation in native space.

  ex. '/home/username/data/derived_data/native_lobes_T1w.nii.gz'
  

• mni_lobes (a pathlike object or string representing a file)

  Lobes segmentation in MNI space.

  ex. '/home/username/data/derived_data/mni_lobes_T1w.nii.gz'
  

• native_tissues (a pathlike object or string representing a file)

  Tissues segmentation in native space.

  ex. '/home/username/data/derived_data/native_tissues_T1w.nii.gz'
  

• mni_tissues (a pathlike object or string representing a file)

  Tissues segmentation in MNI space.

  ex. '/home/username/data/derived_data/mni_tissues_T1w.nii.gz'
  

• matrix_affine (a pathlike object or string representing a file)

  ITK transformation matrix from native to MNI space

  ex. '/home/username/data/derived_data/matrix_affine_native_to_mni_T1w.txt'
  

• report_pdf (a pathlike object or string representing a file)

  Volumetry report (PDF format)

  ex. '/home/username/data/derived_data/report_T1w.pdf'
  

• report_csv (a pathlike object or string representing a file)

  Volumetry report (csv format)

  ex. '/home/username/data/derived_data/report_T1w.csv'
  

---

Usefull links:

volBrain Assemblynet

brainCOLOR protocol

Docker