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iso2mesh specifications


Unique identifier OMICS_29787
Name iso2mesh
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A 3D binary image.
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.8.0
Stability Stable
Maintained Yes




No version available


  • person_outline Qianqian Fang <>

Publication for iso2mesh

iso2mesh citations


Three dimensional architecture of the whole human soleus muscle in vivo

PMCID: 5910694
PMID: 29682414
DOI: 10.7717/peerj.4610

[…] in volume between muscle lengths presumably indicate errors in segmentation., from the segmentations, 3d triangulated surface models were created for all compartments using the matlab-based iso2mesh toolbox ( and ; ). muscle volume of each compartment was calculated as the volume of the surface models. muscle length was calculated as the distance between the most proximal […]


Subject specific multi poroelastic model for exploring the risk factors associated with the early stages of Alzheimer's disease

PMCID: 5740222
PMID: 29285346
DOI: 10.1098/rsfs.2017.0019

[…] algorithms, including both publicly available sources in addition to newly developed ones. the references for the tools used in this workflow can be found in [] (tortoise), [] (niftyreg) and [] (iso2mesh). the first step of this workflow is image segmentation, which features detailed subcortical (including the ventricular system) and whole-brain segmentation of t1w-mr images. fully automatic […]


Quality improvement of surface triangular mesh using a modified Laplacian smoothing approach avoiding intersection

PMCID: 5590917
PMID: 28886110
DOI: 10.1371/journal.pone.0184206

[…] cavities. the fifth column shows the cpu time cost by deleting the redundant points and doing laplacian smoothing., we compared the mesh quality of the improved meshes by our smopt with those by iso2mesh []. iso2mesh is a free matlab/octave-based mesh generation and processing toolbox. we use the meshresample and smoothsurf modules in iso2mesh to improve the initial meshes. to make […]


The Effect of a Transcranial Channel as a Skull/Brain Interface in High Definition Transcranial Direct Current Stimulation—A Computational Study

PMCID: 5233984
PMID: 28084429
DOI: 10.1038/srep40612

[…] (). the diameters of the shaft varied from 1 to 9 mm and we set the diameter of the hat to the shaft diameter +1 mm., 3d-optimized tetrahedral volume mesh was constructed from the surface mesh using iso2mesh and tetgen. there were approximately 18 million total tetrahedral elements, with far smaller elements distributed around the electrode, transcranial channel, and regions of interest (rois) […]


Within brain area tractography suggests local modularity using high resolution connectomics

PMCID: 5213837
PMID: 28054634
DOI: 10.1038/srep39859

[…] the pial surface files (id_3t_structural_preproc_extended/id/t1w/id/surf/* preprocessed from the hcp data available at using the matlab software package “iso2mesh” by 90%. the resulting mesh has around 50,000 triangles (nodes in the network) with a mean surface area of 3.25 mm2 (see ). downsampling has the benefit of making the subsequent network […]


Incorporating and Compensating Cerebrospinal Fluid in Surface Based Forward Models of Magneto and Electroencephalography

PMCID: 4966911
PMID: 27472278
DOI: 10.1371/journal.pone.0159595

[…] the inner and outer boundaries of the skull (inner skull, outer skull), and the outer scalp boundary (scalp). the original surface meshes were slightly smoothed using “smoothsurf” function of iso2mesh toolbox [] and a segmentation error at the scalp base was manually corrected., head 2 was built from a structural mri dataset that had been collected for the nih human connectome project […]

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iso2mesh institution(s)
Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
iso2mesh funding source(s)
Supported by NIH R01EB006385 and R01CA097305.

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