Package pbj details

Parametric Bootstrap Joint Testing Procedures for Neuroimaging

These parametric bootstrap joint (PBJ) inference procedures are designed for the analysis of neuroimaging data. The statistical tools are more generally applicable, but this package is designed to allow input and output data for (Neuroimaging Informatics Technology Initiative) NIfTI images. The PBJ tools are designed for voxel-wise and cluster-extent hypothesis testing methods and include semi-PBJ (sPBJ) inference that is robust to variance misspecification using an estimating equations approach. [see Vandekar, Simon N., Satterthwaite, Theodore D., Xia, Cedric H., Ruparel, Kosha, Gur, Ruben C., Gur, Raquel E., Shinohara, Russell T.. 2018. "Robust Spatial Extent Inference with a Semiparametric Bootstrap Joint Testing Procedure}". ] or [Vandekar, Simon N., Satterthwaite, Theodore D. and Rosen, Adon and Ciric, Rastko and Roalf, David R. and Ruparel, Kosha and Gur, Ruben C. and Gur, Raquel E. and Shinohara, Russell T.. 2018. "Faster family-wise error control for neuroimaging with a parametric bootstrap". Biostatistics. 19(4):497-513. ]. .

Maintainer: Simon Vandekar < simon.vandekar at >

From within R, enter citation(pbj)

Maumet C, Auer T, Bowring A, Chen G, Das S, Flandin G, Ghosh S, Glatard
T, Gorgolewski KJ, Helmer KG, Jenkinson M, Keator DB, Nichols BN,
Poline J, Reynolds R, Sochat V, Turner J, Nichols TE (2016). "Sharing
brain mapping statistical results with the neuroimaging data model."
_Scientific Data_, *3*. ISSN 2052-4463, doi: 10.1038/sdata.2016.102
(URL:, .

Gorgolewski KJ, Varoquaux G, Rivera G, Schwarz Y, Ghosh SS, Maumet C,
Sochat VV, Nichols TE, Poldrack RA, Poline J, Yarkoni T, Margulies DS
(2015). " a web-based repository for collecting and
sharing unthresholded statistical maps of the human brain." _Frontiers
in Neuroinformatics_, *9*. ISSN 1662-5196, doi:
10.3389/fninf.2015.00008 (URL:, .

Muschelli J, Gherman A, Fortin J, Avants B, Whitcher B, Clayden JD,
Caffo BS, Crainiceanu CM (2018). "Neuroconductor: an R platform for
medical imaging analysis." _Biostatistics_. doi:
10.1093/biostatistics/kxx068 (URL:, .

Vandekar SN, Satterthwaite TD, Xia CH, Ruparel K, Gur RC, Gur RE,
Shinohara RT (2018). "Robust Spatial Extent Inference with a
Semiparametric Bootstrap Joint Testing Procedure." _arXiv:1808.07449
[stat]_. arXiv: 1808.07449, .

Sommerfeld M, Sain S, Schwartzman A (2018). "Confidence regions for
spatial excursion sets from repeated random field observations, with an
application to climate." _Journal of the American Statistical
Association_, 1-14.

To see these entries in BibTeX format, use 'print(,
bibtex=TRUE)', 'toBibtex(.)', or set


If you have any problems with this package you can open a new issue or check the already existing ones here.

To install this package, start R and enter:


# Default Install

# From the Binary Repo in NeuroC
neuro_install('pbj', release = "stable", release_repo = binary_release_repo(release = "stable"))
neuro_install('pbj', release = "current", release_repo = binary_release_repo(release = "current"))

# from GitHub
neuro_install('pbj', release = "stable", release_repo = "github")
neuro_install('pbj', release = "current", release_repo = "github")

More detailed installation instructions can be found here.


Initially submitted on April 19 2019 11:24AM
Last updated on July 21 2019 12:01AM
Package type standard
Source GitHub GitHub
Neuroconductor GitHub GitHub
DependsR (3.3)
Importsabind, fslr, mgcv, mmand, parallel, RNifti, R.rsp, utils
LinkingToRcpp (0.12.18), RcppArmadillo
Suggestsknitr, rmarkdown