NiftySeg specifications


Unique identifier OMICS_17569
Name NiftySeg
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.9.4
Stability Stable
Maintained Yes



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NiftySeg in publications

PMCID: 5440179
PMID: 28286318
DOI: 10.1016/j.neuroimage.2017.03.010

[…] segmentations with a low amount or absence of fp, while low ppv values represent over-segmented results., skeletonized measures were calculated using the spinal cord toolbox () and the others using niftyseg ( msd, hsd, shd and smd are presented in millimetres, with lower scores reflecting better results. finally, for dsc, ji, cc, tnr, tpr and ppv, higher scores reflect better […]

PMCID: 5409096
PMID: 28093491
DOI: 10.1093/hmg/ddx003

[…] approach, similarity and truth estimation for propagated segmentations (,), employing an external mouse brain atlas database () and open-source registration and segmentation software, niftyreg and niftyseg (available: to align equivalent anatomical regions between subjects, we performed group-wise registration of all brain images, using niftyreg […]

PMCID: 5082365
PMID: 27786306
DOI: 10.1038/srep36151

[…] the segmentation performance degraded rapidly in the presence of pathology (e.g. ms lesions), not allowing to use the default application over ms subjects. opal is publicly available inside niftyseg software package (, the main characteristic of steps is that it introduces a spatially variant image similarity term in a staple framework, enabling the characterisation […]

PMCID: 4988790
PMID: 27377222
DOI: 10.1016/j.neuroimage.2016.06.053

[…] region, thus removing of spurious edges that might affect further analysis pipelines, e.g. atrophy estimation., the presented algorithm has been included as standalone tool in the software package niftyseg ( and as web-service at, for the multi-time-point filling, we first calculate the transformation from each time-point to the average […]

PMCID: 5033246
PMID: 27658297
DOI: 10.1371/journal.pone.0162974

[…] differences without the laborious delineation of regions of interest. we show the application of freely available open-source software developed for clinical mri analysis to mouse brain data: niftyseg for segmentation and niftyreg for registration, and discuss atlases and parameters suitable for the preclinical paradigm. we used this pipeline to compare 29 tc1 brains with 26 wild-type […]

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