Neuroconductor Release Docker Image

The Docker image for the latest stable release (May2020) is now available.

Why did we do this?

Docker is a very popular container platform which can be run on a multitude of platforms (UNIX, MAC, Windows), on laptops, desktops or even on cloud instances. Given the complexity of some of the Neuroconductor packages and taking into account that some of them are not yet compatible with the Windows platform, we've decided to provide all of our users with an already set up Neuroconductor Docker image that contains the required system dependencies as well as all the Neuroconductor Packages. Our goal was to alleviate the pain of having to setup all the system requirements and packages while at the same time ensuring that we offer a stable solution for conducting reproducible research. This image is based on our most recent release and we will continue to update it as we push new releases.

Use Instructions
  • To download the image Docker client needs to be installed locally. Clients for Mac, UNIX and Windows can be found at Installation is straight forward and should not take too long.
  • Once the Docker client is installed the next step is to open a terminal window. Please use this guide if you are not sure how to do so.
  • Next step is to pull the Neuroconductor Docker image locally. This can be accomplished from the terminal window please use the following command (you can copy paste it from here) docker pull adigherman/neuroconductor-release
  • Once the image was downloaded you can connect to it by running the following command: docker run -it adigherman/neuroconductor-release /bin/bash

Image Specs:

aal 0.1.1 Automated Anatomical Labeling (AAL) Atlas
afnir 0.4.6 Wrapper Functions for AFNI (Analysis of FunctionalNeuroImages)
alvin 0.3.0 ALVIN Ventricle Atlas
ANTsR ANTs in R: Quantification Tools for Biomedical Images
ANTsRCore 0.7.4 Core Software Infrastructure for ANTsR
aws 2.4.1 Adaptive Weights Smoothing
bftools 0.2.2 BioFormats Tools
brainKCCA 0.1.0 Region-Level Connectivity Network Construction via Kernel Canonical Correlation Analysis
brainR 1.6.0 Helper Functions to 'misc3d' and 'rgl' Packages for Brain Imaging
cap 0.1.0 Covariate Assisted Principal (CAP) Regression for CovarianceMatrix Outcomes
cfma 1.0.1 Causal Functional Mediation Analysis
cifti Toolbox for Connectivity Informatics Technology Initiative(CIFTI) Files
clever 0.1.5 Calculate Leverage of Component Models
dcemriS4 0.57.2 A Package for Image Analysis of DCE-MRI (S4 Implementation)
dcm2niir Conversion of DICOM to NIfTI Imaging Files Through R
dcmsort 0.3.0 Sort DICOM Images
dcmtk Wrapper for DICOM Toolkit (DCMTK)
DensParcorr 1 Dens-Based Method for Partial Correlation Estimation in LargeScale Brain Networks
divest 0.8.2 Get Images Out of DICOM Format Quickly
dti 1.5.1 Analysis of Diffusion Weighted Imaging (DWI) Data
eegUtils A collection of utilities for EEG analysis
EveTemplate 1.0.0 JHU-MNI-ss (Eve) template
extrantsr 3.9.13 Extra Functions to Build on the ANTsR Package
flexconn FLEXCONN Model
fmri 1.9.3 Analysis of fMRI Experiments
fmriqa 0.4.0 Functional MRI Quality Assurance Routines
freesurfer 1.6.5 Wrapper Functions for Freesurfer
fslr 2.24.4 Wrapper Functions for FSL (FMRIB Software Library) fromFunctional MRI of the Brain (FMRIB)
gganatogram 1.1.1 Create Anatograms of Various Species
ggBrain 0.1 ggplot Brain Images
ggneuro 0.5.0 Plotting Functions for Neuroimaging Data in ggplot2
ggseg 1.5.3 Plotting tool for brain atlases
gifti Reads in Neuroimaging GIFTI Files with Geometry Information
I2C2 0.2.4 Image Intraclass Correlation Coefficient
ichseg 0.17.1 Intracerebral Hemorrhage Segmentation of X-Ray ComputedTomography (CT) Images
ITKR 0.5.3 ITK in R
itksnapr 2.1 Package of ITK-SNAP
kirby21.asl 1.7.0 Example ASL Data from the Multi-Modal MRI ReproducibilityResource
kirby21.base Example Data from the Multi-Modal MRI Reproducibility Resource
kirby21.det2 1.7.0 Example DET2 Structural Data from the Multi-Modal MRIReproducibility Resource
kirby21.dti 1.7.0 Example DTI Data from the Multi-Modal MRI ReproducibilityResource
kirby21.flair 1.7.0 Example FLAIR Structural Data from the Multi-Modal MRIReproducibility Resource
kirby21.fmri 1.7.0 Example Functional Imaging Data from the Multi-Modal MRIReproducibility Resource
kirby21.mricloud A dataset containing correlation data for 20 subjects fromKennedy Krieger 1.7.0 MT Structural Data from the Multi-Modal MRI ReproducibilityResource
kirby21.smri 1.5 Example Structural Data from the Multi-Modal MRI Reproducibility Resource
kirby21.t1 1.7.0 Example T1 Structural Data from the Multi-Modal MRIReproducibility Resource
kirby21.t2 1.7.0 Example T2 Structural Data from the Multi-Modal MRIReproducibility Resource
kirby21.vaso 1.7.0 Example VASO Data from the Multi-Modal MRI ReproducibilityResource
LESYMAP Lesion to Symptom Mapping in R
LINDA 0.5.1 Lesion Identification with Neighborhood Data Analysis
lungct Processing of Lung Computed Tomography (CT) Scans
malf.templates 1.2.0 Template Images for Multi-Atlas Label Fusion (MALF)
medals 0.3.0 Performs Memory Efficient Decomposition for Analysis of Localneighborhood moments for Segmentation
mimosa 0.5.8 MIMoSA: A Method for Inter-Modal Segmentation Analysis
mmand 1.6.0 Mathematical Morphology in Any Number of Dimensions
mni 0.2.0 Human MNI (Montreal Neurological Institute) Adult Templates
MNITemplate 1.0.0 MNI MRI Template
MriCloudR 0.9.3 R wrapper for MriCloud API
MRIcloudT1volumetrics 0.3.1 MRIcloud Analysis of T1 Volumetric Output
msmri 0.3.1 Open Multiple Sclerosis Magnetic Resonance Imaging Data
neurobase 1.30.0 Neuroconductor Base Package with Helper Functions for niftiObjects
neurocInstall 0.12.1 Neuroconductor Installer
neurocStats 0.1.2 Package that Retrieves Neuroconductor Stats
neurohcp 0.8.1 Human Connectome Project Interface
neurovault 0.5.6 Neurovault Database API Access
NiftiArray HDF5 Delayed Array for Nifti Objects
nitrcbot 1.2 Download Image Files from the NeuroImaging Tools and ResourcesCollaboratory
nsrr 0.1.5 Interface to National Sleep Research Resource
oasis 3.0.1 Multiple Sclerosis Lesion Segmentation using Magnetic ResonanceImaging (MRI)
oro.asl 0.1.1 Rigorous - Aterial Spin Labelling
oro.dicom Rigorous - DICOM Input / Output
oro.nifti 0.10.2 Rigorous - NIfTI + ANALYZE + AFNI : Input / Output 0.2.5 Rigorous - Positron Emission Tomography
pain21 0.1.1 21 Pain Studies
papayar 1 View Medical Research Images using the Papaya JavaScript Library
papayaWidget 0.7.1 Embed an Papaya Image Viewer
pbj 0.1.6 Parametric Bootstrap Joint Testing Procedures for Neuroimaging
penn115 0.1.1 Template MRI Scan from 115 University of Pennsylvania Patients
qMRI 1.2 Methods for Quantitative Magnetic Resonance Imaging ('qMRI')
radtools Utilities for Convenient Extraction of Medical Image Metadata
RAVEL 1.2.2 Removal of Artificial Voxel Effect by Linear Regression
RAVELData 0.99.1 Example dataset of input data for RAVEL
rcamino 0.6.4 Port of the Camino Software
RIA 1.4.2 Radiomics Image Analysis Toolbox for Medial Images
RNifti 1.1.0 Fast R and C++ Access to NIfTI Images
RNiftyReg 2.6.7 Image Registration Using the NiftyReg Library
robex Robust Brain Extraction ('ROBEX')
ROpenCVLite 0.3.410 Install OpenCV
rtapas 0.2.0 TAPAS: A thresholding approach for probability map automatic segmentation automatic segmentation
Rvision 0.3.5 Basic Computer Vision Library
Rxnat 1.0.8 Queries and Extracts Images from Extensible Neuroimaging ArchiveToolkit Public/Private Datasets
smri.process 0.8.4 Processing of Structural Magnetic Resonance Imaging
spant 1.2.1 MR Spectroscopy Analysis Tools
spm12r 2.8.1 Wrapper Functions for SPM (Statistical Parametric Mapping)Version 12 from the Wellcome Trust Centre for Neuroimaging
sri24 0.1.2 SRI24 MRI Atlas for Normal Adult Brain Anatomy
stapler 0.7.2 Simultaneous Truth and Performance Level Estimation
sublime0 1.3 Automatic Lesion Incidence Estimation and Detection using Multi-Modality Longitudinal Magnetic Resonance Images
voxel 1.3.5 Mass-Univariate Voxelwise Analysis of Medical Imaging Data
waveslim 1.8.0 Basic Wavelet Routines for One-, Two-, and Three-DimensionalSignal Processing
WhiteStripe 2.3.2 White Matter Normalization for Magnetic Resonance Images usingWhiteStripe