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JIST specifications


Unique identifier OMICS_26156
Alternative name Java Image Science Toolkit
Software type Application/Script
Interface Command line interface, Application programming interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 3.2
Stability Stable
Maintained Yes




No version available

Additional information

https://www.nitrc.org/projects/jist/ https://idoimaging.com/programs/32

Publication for Java Image Science Toolkit

JIST citations


Quantitative spinal cord MRI in radiologically isolated syndrome

PMCID: 5773843
PMID: 29359174
DOI: 10.1212/NXI.0000000000000436

[…] mtr (figure e-1 at http://links.lww.com/nxi/a25)., each diffusion-weighted image was registered to the initial b0 volume using a 6 degree-of-freedom, rigid-body registration in flirt using the java image science toolkit. the diffusion tensor and maps of dti indices (fractional anisotropy [fa], mean diffusivity [md], perpendicular diffusivity [λ⊥], and parallel diffusivity [λ||]), […]


Longitudinal MR spectroscopy of neurodegeneration in multiple sclerosis with diffusion of the intra axonal constituent N acetylaspartate

PMCID: 5496488
PMID: 28702353
DOI: 10.1016/j.nicl.2017.06.028

[…] injected by power injector (medrad, warrendale, pa) over a period of 60 s., t1-weighted, flair and dti volumes were processed in mipav () (medical image processing, analysis and visualization) and jist () (java image science toolbox). the t1-weighted and flair images within an acquisition were rigidly registered to each other and subsequently to the montreal neurological institute (mni) atlas […]


A Systematic Relationship Between Functional Connectivity and Intracortical Myelin in the Human Cerebral Cortex

PMCID: 5390400
PMID: 28184415
DOI: 10.1093/cercor/bhx030

[…] and analyses were performed on linux servers running ubuntu 12.04.5 lts. the following software tools were used for data processing: cbs tools (v3.0, ) as a plugin for mipav (v7.0.1, ) and jist (v2.0, ), ants (v2.1.0, ), nipype (v0.11.0, ), nilearn (v0.2.3, ), meshlab (v1.3.0, meshlab.sourceforge.net), freesurfer (v5.3.0, ; ), and afni (v16.1.28, ). custom scripts were written […]


Relating multi sequence longitudinal intensity profiles and clinical covariates in incident multiple sclerosis lesions

PMCID: 4660378
PMID: 26693397
DOI: 10.1016/j.nicl.2015.10.013

[…] the scanning parameters were clinically optimized for each acquired image., for image preprocessing, we use medical image processing analysis and visualization (http://mipav.cit.nih.gov) and the java image science toolkit (http://www.nitrc.org/projects/jist) (). we interpolate all images for each subject at each visit to a voxel size of 1 mm3 and rigidly co-register all volumes […]


Parallel workflow tools to facilitate human brain MRI post processing

Front Neurosci
PMCID: 4429548
PMID: 26029043
DOI: 10.3389/fnins.2015.00171

[…] automated workflows for any purpose by linking either modules from predefined libraries or in-house modules, such as laboratory of neuro imaging (loni) pipeline (rex et al., ; dinov et al., , ), java image science toolkit (jist) (lucas et al., ; li et al., ) and nipype (gorgolewski et al., ). the other category is fixed workflow tools that provide a completely established data processing […]


Statistical normalization techniques for magnetic resonance imaging☆☆☆

PMCID: 4215426
PMID: 25379412
DOI: 10.1016/j.nicl.2014.08.008

[…] 3 t scanners described elsewhere (). all image preprocessing was conducted using the medical image processing, analysis and visualization (http://mipav.cit.nih.gov) software environment through the java image science toolkit (). all images were corrected for spatial inhomogeneity () and rigidly aligned across modalities at each study visit to the montreal neurological institute template. […]

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JIST institution(s)
Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA; National Institute on Aging, National Institute of Health, Baltimore, MD, USA; Department of Radiology and Radiological Science, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA; Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA
JIST funding source(s)
Supported by NIH/NINDS 5R01NS037747 and 1R01NS056307 and NIH/NIA N01-AG-4-0012.

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