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Bpipe specifications


Unique identifier OMICS_02301
Name Bpipe
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Groovy, Java, Shell (Bash)
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes




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  • person_outline Simon Sadedin

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Publication for Bpipe

Bpipe citations


Neuroanatomical and Symptomatic Sex Differences in Individuals at Clinical High Risk for Psychosis

PMCID: 5744013
PMID: 29312018
DOI: 10.3389/fpsyt.2017.00291

[…] with a field of view of 256 mm, repetition time of 22 ms, echo time of 9.2 ms, and flip angle of 30°., t1-weighted mr images were converted to the minc file format and processed using the minc-bpipe-library pre-processing pipeline from the cobra laboratory tools. pre-processing consisted of a two-step whole-scan bias field correction, with and without an approximate brain mask using n4itk […]


Playing Super Mario 64 increases hippocampal grey matter in older adults

PLoS One
PMCID: 5718432
PMID: 29211727
DOI: 10.1371/journal.pone.0187779

[…] to neuroanatomy that measures differences in the local density of brain tissue through a voxel-wise comparison of multiple brain images []. mri images were run through a bioinformatics pipeline (bpipe). the images were first corrected for intensity non-uniformity (shading artifacts) using the n4 software package [] and then spatially normalized by linear transformation using icbm 152 atlases […]


Cerebellar anatomical alterations and attention to eyes in autism

Sci Rep
PMCID: 5607223
PMID: 28931838
DOI: 10.1038/s41598-017-11883-w

[…] in the isolation map of the suit pipeline located in the anterior cerebellum., prior to the cerebellar parcellation with the maget brain pipeline, we preprocessed (https://github.com/cobralab/minc-bpipe-library) the t1 images and performed n4 correction, cutneck and registration to the mni space using the advanced normalization tools (ants) software. the maget brain pipeline uses five high […]


Association of monoamine oxidase A genetic variants and amygdala morphology in violent offenders with antisocial personality disorder and high psychopathic traits

Sci Rep
PMCID: 5575239
PMID: 28851912
DOI: 10.1038/s41598-017-08351-w

[…] (ge medical systems, milwaukee, wi)., all t1-weighted mri data were converted to the minc file format (http://www.bic.mni.mcgill.ca/servicessoftware/minc) and underwent preprocessing using the bpipe tools from the cobra laboratory (https://github.com/cobralab/minc-bpipe-library). this process included rigid (6-parameter) registration to mni space, cropping of the neck region to improve […]


Investigating reproducibility and tracking provenance – A genomic workflow case study

BMC Bioinformatics
PMCID: 5508699
PMID: 28701218
DOI: 10.1186/s12859-017-1747-0

[…] pipelines on remote servers without requiring access to gui so that they are easily administered through source code management tools []. however, the command line based pipeline frameworks such as bpipe [], snakemake [] and ruffus [] used to develop these systems are not flexible enough to support integration of new user-defined steps and analysis tools. working with such systems requires […]


The effect of crack cocaine addiction and age on the microstructure and morphology of the human striatum and thalamus using shape analysis and fast diffusion kurtosis imaging

PMCID: 5534960
PMID: 28485734
DOI: 10.1038/tp.2017.92

[…] total scan time was ~50 min., t1-weighted images were converted from dicom format to minc for preprocessing. t1 images were preprocessed using an in-house preprocessing pipeline with the software bpipe (http://cobralab.ca/software/mincbeast_bpipe.html), which makes use of the minc tool-kit (http://www.bic.mni.mcgill.ca/servicessoftware/servicessoftwareminctoolkit) and advanced normalization […]

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Bpipe institution(s)
Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia; Victorian Life Sciences Computation Initiative, The University of Melbourne, Carlton, VIC, Australia

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