CALAMITI

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Contrast Anatomy Learning and Analysis for MR Intensity Translation and Integration (CALAMITI)

Contrast Anatomy Learning and Analysis for MR Intensity Translation and Integration (CALAMITI) is our current MR harmonization method. It was designed to achieve unsupervised multi-site MR harmonization. The associated publication is:

Software

CALAMITI (2D) 220k
CALAMITI (3D) Coming soon

Instructions

Preprocessing

CALAMITI requires the following preprocessing steps:

Prepare training

CALAMITI requires paired multi-contrast MR images (e.g., T1-w and T2-w) during training. The ideal structure of the data directory and naming convention are as follows:

   ├──absolute_path_to_data
       ├──SiteA
       |    ├──train
       |    |    ├──SiteA_T1w_SUB*_ORIENTATION_SLICE*.nii.gz ("ORIENTATION" should be "AXIAL", "CORONAL", or "SAGITTAL")
       |    |    └──SiteA_T2w_SUB*_ORIENTATION_SLICE*.nii.gz
       |    └──valid
       |         ├──SiteA_T1w_SUB*_ORIENTATION_SLICE*.nii.gz 
       |         └──SiteA_T2w_SUB*_ORIENTATION_SLICE*.nii.gz
       └──SiteB
           ├──train
           |    ├──SiteB_T1w_SUB*_ORIENTATION_SLICE*.nii.gz 
           |    └──SiteB_T2w_SUB*_ORIENTATION_SLICE*.nii.gz
           └──valid
                ├──SiteB_T1w_SUB*_ORIENTATION_SLICE*.nii.gz
                └──SiteB_T2w_SUB*_ORIENTATION_SLICE*.nii.gz

Sample command and dependencies

  • After downloading the code, sample command for CALAMITI training and testing (encoding and decoding) can be found in "script" folder.
  • Conda environment can be downloaded here.

If you have other questions regarding the method or software, please email Lianrui Zuo at lr_zuo@jhu.edu