ITK-SNAP protocols

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ITK-SNAP specifications


Unique identifier OMICS_26149
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Medium
Version 3.6.0
Stability Stable
Registration required Yes
Maintained Yes



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  • person_outline Paul Yushkevich <>

Additional information

Publication for ITK-SNAP

ITK-SNAP in pipelines

PMCID: 5285292
PMID: 28144808
DOI: 10.1186/s10194-016-0715-9

[…] (; (2) individual pag segment by apply the deformation field (generated by segment) to the pag template using the runback strategy; (3) calculate the individual pag volume using itk-snap (v3.6.0-beta) ( (fig. ).fig. 1 , the statistical analysis was performed by using pasw statistics 18.0. the significance differences of pag volume […]

PMCID: 5740223
PMID: 29285347
DOI: 10.1098/rsfs.2017.0021

[…] using a combination of automatic and manual tools [,] including both commercial and open source software: mimics (materialise, belgium), simpleware scanip (synopsis, uk), vmtklab (orobix, italy), itk-snap ( []) and osirix (pixmeo, switzerland). three-dimensional anatomical volumes of the blood pool were created from the 3d whole-heart mr sequences and from ct in order […]

PMCID: 4427777
PMID: 26060504
DOI: 10.1155/2015/167489

[…] dataset [] using the dice similarity index and recall and precision measures. the method was also compared with other popular packages such as freesurfer ([], and itk-snap ([],, the lpba40 dataset was used for validation of the proposed method ([], it consists of 40 […]

PMCID: 4178250
PMID: 25365798
DOI: 10.1002/brb3.271

[…] two criteria; one, that all the aforementioned anatomical features were present and two, that it was selected from between the cerebral hemispheres. manual segmentation of the ica was conducted on itk-snap software (yushkevich et al. ) ( where the sagittal sections were in a significant oblique plane, such that the anatomical features needed for segmentation, […]

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ITK-SNAP in publications

PMCID: 5943199
PMID: 29744748
DOI: 10.1186/s13550-018-0389-1

[…] basis of a method described by khalighi et al. [, ] with the dataset of the subjects from subject group 2, who additionally had contrast-enhanced mri examination. the active contour algorithm from itk snap (version 3.6.0) was used to extract the aorta volume va from the contrast-enhanced mr data. spill-out region was defined by summing up the early pet frames and segmenting the aorta […]

PMCID: 5941431
PMID: 29739350
DOI: 10.1186/s12880-018-0252-x

[…] a noise level of 9% and an inu level of 40% from the brainweb dataset. in the figure, the 2d axial, sagittal and coronal views of 3d segmentation results are shown for visual inspections using the itk-snap tool []. the first and second columns are the image and the ground truth of the segmentation with red, green, blue voxels corresponding to csf, gm and wm tissues, respectively. the third, […]

PMCID: 5936785
PMID: 29760665
DOI: 10.3389/fphys.2018.00458

[…] outline for both the smoothed and detailed geometries., the control lv, as a representative of a state of the art anatomical model, was reconstructed using a regularized region growing algorithm of itk-snap (itk-snap medical image segmentation tool, rrid:scr_002010) to get only large scale anatomical detail from the images. the algorithm allowed controlling the smoothness of the extracted […]

PMCID: 5928106
PMID: 29712947
DOI: 10.1038/s41598-018-24951-6

[…] to the middle volume of a serial acquisition; and (iii) reorienting the brain into left-anterior-superior (las) axes (radiological view). intracranial binary brain masks were created manually using itk-snap 3.4.0 ( for each functional and anatomical dataset and were used to extract the brain using the flsmaths tool. post-stimulation images were co-registered to the baseline fmri […]

PMCID: 5906442
PMID: 29670138
DOI: 10.1038/s41598-018-24549-y

[…] and bilateral anatomically defined rois within the mtl (hippocampal head, body, and tail; perirhinal cortex - prc; parahippocampal cortex - phc). anatomical rois were manually traced using the itk-snap software package ( using established procedures,–. using parameter estimates extracted from these rois, we examined their functional activation profiles across […]

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ITK-SNAP institution(s)
Penn Image Computing and Science Laboratory (PICSL), Department of Radiology, University of Pennsylvania, PA, USA; Departments of Computer Science and Psychiatry, University of North Carolina, NC, USA; Neurodevelopmental Disorders Research Center, University of North Carolina, NC, USA
ITK-SNAP funding source(s)
Supported by Cognitica Corporation under NIH/NLM PO 467-MZ-202446-1, the NIH/NIBIB P01 EB002779, NIH Conte Center MH064065, and UNC Neurodevelopmental Disorders Research Center, Developmental Neuroimaging Core.

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