Difference between revisions of "CALAMITI"

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{{h2|Contrast Anatomy Learning and Analysis for MR Intensity Translation and Integration (CALAMITI)}}
 
{{h2|Contrast Anatomy Learning and Analysis for MR Intensity Translation and Integration (CALAMITI)}}
 
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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:
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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 publications are:
  
 
*{{pub| author = L. Zuo, B.E. Dewey, A. Carass, Y. Liu, Y. He, P.A. Calabresi, and J.L. Prince| title = [https://arxiv.org/abs/2103.13283 Information-based Disentangled Representation Learning for Unsupervised MR Harmonization]| conf = ipmi2021}}
 
*{{pub| author = L. Zuo, B.E. Dewey, A. Carass, Y. Liu, Y. He, P.A. Calabresi, and J.L. Prince| title = [https://arxiv.org/abs/2103.13283 Information-based Disentangled Representation Learning for Unsupervised MR Harmonization]| conf = ipmi2021}}
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*{{pub| author= L. Zuo, B. E. Dewey, Y. Liu, Y. He, S. D. Newsome, E. M. Mowry, S. M. Resnick, J. L. Prince, and A. Carass| title = Unsupervised MR harmonization by learning disentangled representations using information bottleneck theory|  jrnl=ni | number= 118569 | when=2021| doi=10.1016/j.neuroimage.2021.118569}}
  
 
{{h3|Software}}
 
{{h3|Software}}
  
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|-
 
|-
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| {{iacl|~lianrui/calamiti/calamiti_ipmi2021_v1.zip|CALAMITI code (2D)}}
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| {{iacl|~lianrui/calamiti/calamiti_ipmi2021_v1.zip|CALAMITI (2D)}}
 
| 220k
 
| 220k
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|-
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| {{iacl|~lianrui/calamiti_3d/neuroimage_2021_calamiti.zip|CALAMITI (3D)}}
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| 330Mb (including sample data)
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|
 
|-
 
|-
 
|}
 
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If you have questions regarding the method or software, please email Lianrui Zuo at <code>lr_zuo@jhu.edu
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{{h3|Instructions}}
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{{h4|Preprocessing}}
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CALAMITI requires the following preprocessing steps:
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* N4 inhomogeneity correction.
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* Registration to MNI space (0.8mm isotropic resolution is ideal. Image dimension after MNI registration is 241*288*241).
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* White matter peak normalization (see https://github.com/jcreinhold/intensity-normalization).
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{{h4|Prepare training}}
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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:
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    ├──absolute_path_to_data
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        ├──SiteA
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        |    ├──train
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        |    |    ├──SiteA_T1w_SUB*_ORIENTATION_SLICE*.nii.gz ("ORIENTATION" should be "AXIAL", "CORONAL", or "SAGITTAL")
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        |    |    └──SiteA_T2w_SUB*_ORIENTATION_SLICE*.nii.gz
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        |    └──valid
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        |        ├──SiteA_T1w_SUB*_ORIENTATION_SLICE*.nii.gz
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        |        └──SiteA_T2w_SUB*_ORIENTATION_SLICE*.nii.gz
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        └──SiteB
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            ├──train
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            |    ├──SiteB_T1w_SUB*_ORIENTATION_SLICE*.nii.gz
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            |    └──SiteB_T2w_SUB*_ORIENTATION_SLICE*.nii.gz
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            └──valid
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                ├──SiteB_T1w_SUB*_ORIENTATION_SLICE*.nii.gz
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                └──SiteB_T2w_SUB*_ORIENTATION_SLICE*.nii.gz
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{{h4|Sample command and dependencies}}
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* After downloading the code, sample command for CALAMITI training can be found in <code>"script"</code> folder. Testing (encoding and decoding) code can be found in <code>"encode"</code> and <code>"decode"</code>.
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* Conda environment can be downloaded {{iacl|~lianrui/calamiti/calamiti.yml|here}}.
 +
 
 +
If you have other questions regarding the method or software, please email Lianrui Zuo at <code>lr_zuo@jhu.edu

Latest revision as of 19:02, 1 August 2022

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 publications are:

  • L. Zuo, B.E. Dewey, A. Carass, Y. Liu, Y. He, P.A. Calabresi, and J.L. Prince, "Information-based Disentangled Representation Learning for Unsupervised MR Harmonization", 27th Conference on Information Processing in Medical Imaging (IPMI 2021), Virtually in Bornholm, Denmark, June 28 - July 2, 2021.
  • L. Zuo, B. E. Dewey, Y. Liu, Y. He, S. D. Newsome, E. M. Mowry, S. M. Resnick, J. L. Prince, and A. Carass, "Unsupervised MR harmonization by learning disentangled representations using information bottleneck theory", NeuroImage, 118569, 2021. (doi)

Software

CALAMITI (2D) 220k
CALAMITI (3D) 330Mb (including sample data)

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 can be found in "script" folder. Testing (encoding and decoding) code can be found in "encode" and "decode".
  • 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

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