SCIM - an efficient iterative "fusion bootstrap moves" (FBM) solver that enables precise parameter estimates for Intravoxel Incoherent Motion of DWI MRI images in spatially constraint manner.
C++ compiled binaries are available prebuilt as a Docker image. Binaries are also available in bin folder and require centOS to be ran.
See here: example.md
- 1.5T - computes IVIM via MLE cost function, with noise estimated from background regions
- 3T - // with noise fixed at 2
- 3Ti - // with noise input defined by user (NB this needs to be specified for every FBM iteration)
Images are available from
- dockerhub
- BCH google drive (warning: only bch users with access)
/fileserver/external/body/serge/scim/docker
docker pull sergeicu/scim:$version
See bin/
Docker images are based on centos6.
Binaries in bin folder will run on centOS6+ without docker.
To build new docker image see docker/README.md.
Basic explanations of what changes were made to the original C++ code for versions (1.5T, 3T, 3Ti) see changes_to_original_code.md
This code is under Apache 2.0 licensing.
If you use it, please cite one of the following papers:
Reliable estimation of incoherent motion parametric maps from diffusion-weighted MRI using fusion bootstrap moves
Freiman, Moti and Perez-Rossello, Jeannette M and Callahan, Michael J and Voss, Stephan D and Ecklund, Kirsten and Mulkern, Robert V and Warfield, Simon K
Medical Image Analysis 2013
[link | bibtex]
Spatially-constrained probability distribution model of incoherent motion (SPIM) for abdominal diffusion-weighted MRI
Kurugol, Sila and Freiman, Moti and Afacan, Onur and Perez-Rossello, Jeannette M and Callahan, Michael J and Warfield, Simon K
Medical Image Analysis 2016
[link | bibtex]
Spatially-constrained probability distribution model of incoherent motion (SPIM) in diffusion weighted MRI signals of crohn’s disease
Kurugol, Sila and Freiman, Moti and Afacan, Onur and Perez-Rossello, Jeannette M and Callahan, Michael J and Warfield, Simon K
MICCAI 2014
[link | bibtex]
Evaluation of Motion-Compensated Spatially-Constrained IVIM (MC-SCIM) Model of Diffusion-weighted MRI for Assessment of Fibrosis in Crohn’s Disease using Surgical Histopathology Scores
Kurugol, Sila and Freiman, Moti and Goldsmith, Jeffrey and Didier, Ryne and Afacan, Onur and Perez-Rossello, Jeanette M and Callahan, Michael J and Bousvaros, Athos and Warfield, Simon K
ISMRM 2017
[link | bibtex]
Self-supervised IVIM DWI parameter estimation with a physics based forward model
Vasylechko, Serge Didenko and Warfield, Simon K and Afacan, Onur* and Kurugol, Sila*
*contributed equally
MRM 2022
[link | arxiv | bibtex]
If you have any question regarding the usage of this code, or any suggestions to improve it, you can contact us at:
serge.vasylechko@childrens.harvard.edu