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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 in publications

PMCID: 5943734
PMID: 29761018
DOI: 10.1002/brb3.966

[…] 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 […]

PMCID: 5660683
PMID: 29114213
DOI: 10.3389/fnhum.2017.00510

[…] 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 […]

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

[…] 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 <prefix>. third, structural […]

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

[…] francisco, california, united states of america, current address: 1010data, new york, new york, united states of america, current address: føcal, cambridge, massachusetts, united states of america, mindboggle (http://mindboggle.info) is an open source brain morphometry platform that takes in preprocessed t1-weighted mri data and outputs volume, surface, and tabular data containing label, […]

PMCID: 4238047
PMID: 25429357
DOI: 10.1016/j.nicl.2014.11.001

[…] development of neuroinformatics which has materialized in several free as well as commercial image analysis software packages released over the past 15 years: spm, fsl, freesurfer, brainvisa, mindboggle, neuroquant, and neuroqlab, to mention a few., brain morphometry methods ultimately aim to extract imaging biomarker information that characterizes structural patterns of changes across […]

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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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