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Mindboggle specifications


Unique identifier OMICS_13802
Name Mindboggle
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A preprocessed brain MR image data, a labeled cortical surface with labeled cortical and noncortical volumes, a brain volume extraction, segmentation and registration-based labeling
Output data A volume files, a surface meshes and a table
Output format NIfTI, VTK, CSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, MATLAB, Python
Computer skills Advanced
Version 1.0.0
Stability Alpha
Maintained No




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Publications for Mindboggle

Mindboggle citations


Behavioral and neurophysiological abnormalities during cued continuous performance tasks in patients with mild traumatic brain injury

PMCID: 5943734
PMID: 29761018
DOI: 10.1002/brb3.966
call_split See protocol

[…] lt for the study (Fonov et al., ). This means that we will be able to use this template brain as a substitute for the subjects without an individual MRI or as the common brain for group analysis. The Mindboggle (http://mindboggle.info) atlas of FreeSurfer was adopted to apply anatomical labels (Klein & Tourville, ).The length of epoch was 1,200 ms (from −200 to 1,000 ms). The second 100‐ms interva […]


Deep gray matter volume loss drives disability worsening in multiple sclerosis

PMCID: 5838522
PMID: 29331092
DOI: 10.1002/ana.25145

[…] urodegenerative disorders., The template library had 95 MRI brain scans (HCs and patients with AD) with neuroanatomic labels (http://www.neuromorphometrics.com/). This atlas, which is similar to the Mindboggle atlas, was developed to improve the consistency and clarity of the Desikan‐Killiany protocol. To calculate brain masks and exclude segmentation errors outside of the brain, we used STEPS (S […]


Visually Evoked Visual Auditory Changes Associated with Auditory Performance in Children with Cochlear Implants

Front Hum Neurosci
PMCID: 5660683
PMID: 29114213
DOI: 10.3389/fnhum.2017.00510
call_split See protocol

[…] between duration 130–180 ms (exactly covering the N1 component for the ‘sound’ condition) in these ROIs were statistically compared between CI users and controls. These ROIs were defined based on the Mindboggle-atlas implemented in Brainstorm, which relies on automatic parcellation using a surface-based alignment of the cortical folding (). PVC encompassed the lingual gyrus and pericalcarine sulcu […]


Discrete pre processing step effects in registration based pipelines, a preliminary volumetric study on T1 weighted images

PLoS One
PMCID: 5638331
PMID: 29023597
DOI: 10.1371/journal.pone.0186071

[…] on removed) template, for use with images containing head, or just brain, information, respectively. Skull-stripping was done utilizing ANTs and referencing the OASIS-30 template hosted at http://www.mindboggle.info/data.html via antsBrainExtraction.sh –d 3 –a lab_template.nii.gz –e ref_template.nii.gz –m probability_mask.nii.gz –f registration_mask.nii.gz –o . Third, structural scans in M […]


Altered insula–default mode network connectivity in fibromyalgia: a resting state magnetoencephalographic study

PMCID: 5567574
PMID: 28831711
DOI: 10.1186/s10194-017-0799-x

[…] ipant was then morphed into a common source space defined by the Colin27 anatomy []. For the connectivity analysis, we defined regions of interest (ROIs) in the structural T1 template volume by using Mindboggle cortical parcellation [], and selected 12 DMN-related brain regions based on previous studies [, , ], including the bilateral posterior cingulate cortex, precuneus, inferior parietal cortex […]


Mindboggling morphometry of human brains

PLoS Comput Biol
PMCID: 5322885
PMID: 28231282
DOI: 10.1371/journal.pcbi.1005350

[…] Mindboggle performs all of its processing in two open standard formats: NIfTI (.nii.gz; http://nifti.nimh.nih.gov/) for volume images and VTK (.vtk, Visualization Toolkit; http://www.vtk.org/) for sur […]

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Mindboggle institution(s)
Department of Psychiatry and Behavioral Science, Stony Brook University School of Medicine, Stony Brook, NY, USA; Department of Psychiatry, Columbia University, New York, NY, USA; Department of Speech, Language, and Hearing Sciences, Boston University, Boston, MA, USA; Center for Computational Neuroscience and Neural Technology, Boston University, Boston, MA, USA
Mindboggle funding source(s)
This work was supported by the National Institute of Mental Health (grant n°MH084029), the OASIS project (grants n°P50 AG05681, P01 AG03991, R01 AG021910, P50 MH071616, U24 RR021382 and R01 MH56584), the MMRR project (grants n°NCRR P41RR015241, 1R01NS056307, 1R21NS064534-01A109 and 1R03EB012461-01), the NKI project (grant n°R01 MH094639) and the HLN project (grant n°EB000461).

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