JIST protocols

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JIST specifications

Information


Unique identifier OMICS_26156
Name JIST
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
Requirements
MIPAV
Maintained Yes

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Additional information


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

Publication for Java Image Science Toolkit

JIST in pipelines

 (2)
2017
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 […]

2015
PMCID: 4429548
PMID: 26029043
DOI: 10.3389/fnins.2015.00171

[…] and frequently used parameters are set as the default. panda was thoroughly tested and validated by students and collaborators before its official release., flexible (e.g., loni pipeline, jist, and nipype) and fixed (e.g., civet, panda, and dparsf) parallel workflow tools are both widely used in the neuroimaging field. these tools can substantially simplify human brain mri […]


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JIST in publications

 (8)
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||]), […]

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 […]

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 […]

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 […]

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 […]


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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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