8½ Minute Mail 8m30mail.com

Receive-only temporary inbox for manual email verification testing, with an 8-minute-30-second default lifetime and no account required.

XNAT xnat.org

An extensible open-source imaging informatics software platform dedicated to imaging-based research.

XCP-D xcp-d.readthedocs.io

Post-processing and noise regression pipeline picks up right where fMRIprep ends.

templateflow templateflow.org

A modular, version-controlled resource that allows researchers to use templates "off-the-shelf" and share new ones.

mri-watershed surfer.nmr.mgh.harvard.edu

Part of the Freesurfer pipeline.

freeview surfer.nmr.mgh.harvard.edu

Surface and volumetric image viewer in Freesurfer suit. Uses the QT toolkit.

ANTs stnava.github.io

Advanced Normalization Tools includes probabilistic tissue segmentation and machine learning methods based on expert labeled data to order to maximize reliability and consistency of multiple modality image segmentation.

gdcm sourceforge.net

Grassroots DICOM is a C++ library and CLI tool for DICOM medical files.

Qu|Nex qunex.yale.edu

The Quantitative Neuroimaging Environment & Toolbox (QuNex) is an open-source software suite that collectively supports an extensible framework for data organization, preprocessing, quality assurance, and analyses across neuroimaging modalities.

qsiprep qsiprep.readthedocs.io

Configures pipelines for processing diffusion-weighted MRI (dMRI) data.

QMENTA qmenta.com

The all in one imaging platform for your clinical trial.

pydicom pydicom.github.io

Python package and cli tool for inspecting, modifying, and creating DICOM files.

osirix osirix-viewer.com

DICOM database organizer and viewer.

ROBEX nitrc.org

Robust Brain Extraction without parameter tweaking.

mricron nitrc.org

Volumetric viewer that works on windows.

NITRC nitrc.org

NeuroImaging Tools & Resources Collaboratory library of neuroinformatics software and data.

nipy nipy.org

Includes nibabel, nipype, and nilearn.

U of A: Neuroimaging Core Documentation neuroimaging-core-docs.readthedocs.io

Documentation for approaches used and/or developed by the neuroimaging core at the University of Arizona.

NDA nda.nih.gov

National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains.

NCANDA ncanda.org

National Consortium on Alcohol and Neurodevelopment in Adolescence (4000+ MR visits).

MRIQC mriqc.readthedocs.io

Extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.

optibet montilab.psych.ucla.edu

Shell script to combine afni and fsl tools for more robust skull stripping in patient populations.

PNC med.upenn.edu

A population-based sample of over 9500 individuals from the greater Philadelphia area, ages 8-21 years who received medical care at the CHOP network.

LORIS mcin.ca

Longitudinal Online Research and Imaging System is a web-based data and project management software for neuroimaging research studies.

CIVET mcin.ca

An image processing pipeline for fully automated volumetric, corticometric, and morphometric analysis of human brain imaging data.

cbrain mcin.ca

Web-based software that allows neuroimaging researchers to perform computationally intensive analyses on data by connecting them to High-Performance Computing (HPC).

brainhack mattermost.brainhack.org

A mattermoust community of neuroimagers.

Mango mangoviewer.com

Multi-image Analysis GUI is a viewer for medical research images for dcm, nii, surface, etc; version 4.1 released in 2019.

tat2 lncd.github.io

Time-averaged T2* wrapper script using AFNI binaries from lncdtools.

dcmdirtab, dcmtab_bids lncd.github.io

CLI focused, regular expression based, and iteration friendly BIDS conversion pipeline from lncdtools.

Hitchhacker's guide to the brain learn-neuroimaging.github.io

Notes from study planning to reporting and data sharing by way of acquisition, processing, analysis, and quality control.

HCP Pipeline humanconnectome.org

Pipeline scripts implement the Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013.

wb_view humanconnectome.org

Connectome workbench surface file viewer.

DataLad handbook handbook.datalad.org

Start-to-end use cases of specific applications in neuroimaging using provenance tracking software datalad.

niinote github.com

Add AFNI nifti XML history to header to run and record any command. Part of lncdtools.

med2image github.com

Python CLI tool for generating jpg or png images from DICOM or nifti files.

pymapVBVD git.fmrib.ox.ac.uk

Reads Siemens .dat 'twix' raw data files. Python port of Philipp Ehses' Matlab tool mapVBVD.

fslmaths fsl.fmrib.ox.ac.uk

Simple but powerful program to allow mathematical manipulation of images. From FSL.

fsleyes fsl.fmrib.ox.ac.uk

Volumetric viewer from FSL.

FSL-MRS fsl.fmrib.ox.ac.uk

A suite of tools for MR Spectroscopy, including single voxel (SVS), MRS imaging (MRSI), functional MRS (fMRS), diffusion MRS (dwMRS), edited spectroscopy, etc.

flirt, fnirt fsl.fmrib.ox.ac.uk

Warping software provided by FSL tools.

FEAT fsl.fmrib.ox.ac.uk

GUI guided analysis of simple experiment based on general linear modeling. Part of FSL.

bet fsl.fmrib.ox.ac.uk

FSL's brain extraction tool.

FSL fsl.fmrib.ox.ac.uk

A comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data.

make frontiersin.org

follow script recipes defined in Makefile.

fscalc freesurfer.net

Freesurfer wrapper of fslmaths.

Freesurfer freesurfer.net

An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.

fooof fooof-tools.github.io

Fast, efficient, and physiologically-informed tool to parameterize neural power spectra.

fmriprep fmriprep.org

Accessible preprocessing pipeline robust to variations in scan acquisition protocols with comprehensive error and output reporting. Input is BIDS dataset.

Flywheel flywheel.io

A cloud-based imaging research data platform for data capture, curating, automation, and machine learning.