Neuroimaging
91 items from npacore/awesome-neuroimaging ★51
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ROBEX nitrc.org
Robust Brain Extraction without parameter tweaking.
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mricron nitrc.org
Volumetric viewer that works on windows.
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NITRC nitrc.org
NeuroImaging Tools & Resources Collaboratory library of neuroinformatics software and data.
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nipy nipy.org
Includes nibabel, nipype, and nilearn.
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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.
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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.
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NCANDA ncanda.org
National Consortium on Alcohol and Neurodevelopment in Adolescence (4000+ MR visits).
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MRIQC mriqc.readthedocs.io
Extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.
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optibet montilab.psych.ucla.edu
Shell script to combine afni and fsl tools for more robust skull stripping in patient populations.
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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.
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LORIS mcin.ca
Longitudinal Online Research and Imaging System is a web-based data and project management software for neuroimaging research studies.
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CIVET mcin.ca
An image processing pipeline for fully automated volumetric, corticometric, and morphometric analysis of human brain imaging data.
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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).
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brainhack mattermost.brainhack.org
A mattermoust community of neuroimagers.
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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.
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tat2 lncd.github.io
Time-averaged T2* wrapper script using AFNI binaries from lncdtools.
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dcmdirtab, dcmtab_bids lncd.github.io
CLI focused, regular expression based, and iteration friendly BIDS conversion pipeline from lncdtools.
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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.
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HCP Pipeline humanconnectome.org
Pipeline scripts implement the Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013.
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wb_view humanconnectome.org
Connectome workbench surface file viewer.
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DataLad handbook handbook.datalad.org
Start-to-end use cases of specific applications in neuroimaging using provenance tracking software datalad.
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niinote github.com
Add AFNI nifti XML history to header to run and record any command. Part of lncdtools.
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med2image github.com
Python CLI tool for generating jpg or png images from DICOM or nifti files.
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pymapVBVD git.fmrib.ox.ac.uk
Reads Siemens .dat 'twix' raw data files. Python port of Philipp Ehses' Matlab tool mapVBVD.
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fslmaths fsl.fmrib.ox.ac.uk
Simple but powerful program to allow mathematical manipulation of images. From FSL.
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fsleyes fsl.fmrib.ox.ac.uk
Volumetric viewer from FSL.
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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.
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flirt, fnirt fsl.fmrib.ox.ac.uk
Warping software provided by FSL tools.
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FEAT fsl.fmrib.ox.ac.uk
GUI guided analysis of simple experiment based on general linear modeling. Part of FSL.
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bet fsl.fmrib.ox.ac.uk
FSL's brain extraction tool.
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FSL fsl.fmrib.ox.ac.uk
A comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data.
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make frontiersin.org
follow script recipes defined in Makefile.
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fscalc freesurfer.net
Freesurfer wrapper of fslmaths.
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Freesurfer freesurfer.net
An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.
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fooof fooof-tools.github.io
Fast, efficient, and physiologically-informed tool to parameterize neural power spectra.
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fmriprep fmriprep.org
Accessible preprocessing pipeline robust to variations in scan acquisition protocols with comprehensive error and output reporting. Input is BIDS dataset.
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Flywheel flywheel.io
A cloud-based imaging research data platform for data capture, curating, automation, and machine learning.
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FIRMM firmm.readthedocs.io
Real-time motion monitoring for fMRI, diffusion, and navigated T1/T2 image acquisition.
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ENIGMA enigma.ini.usc.edu
The Enhancing Neuro Imaging Genetics through Meta Analysis Consortium contains 50 working group's imaging and genomics data.
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PACS en.wikipedia.org
Picture Archiving and Communication System standard used to store and transfer DICOM images from medical equipment and likely implemented by scanner manufacture. See Siemens Healthineers Syngo Carbon, Phillips Vue PACS, GE HealthCare True PACS.
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dsistudio dsi-studio.labsolver.org
DSI viewer from the dsi-studio suit of tools.
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dsi-studio dsi-studio.labsolver.org
A tractography software tool that maps brain connections and correlates findings with neuropsychological disorders.
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antsBrainExtraction.sh dpaniukov.github.io
ANTs version.
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afni discuss discuss.afni.nimh.nih.gov
AFNI's discuss instance.
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reproIn dbic-handbook.readthedocs.io
Naming exam card sequences.
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clpipe clpipe.readthedocs.io
Uses fmriprep for preprocessing fMRI data and implements a variety of additional processing steps important for functional connectivity analyses such as nuisance regression and filtering.
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brainlife.io brainlife.io
Open-source, free and secure reproducible neuroscience analysis platform.
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BIDS bids-specification.readthedocs.io
Brain Imaging Data Structure - directory hierarchy and file naming specification.
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MNI152 bic.mni.mcgill.ca
Unbiased standard magnetic resonance imaging template brain volume for normal population.
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dicom_hinfo afni.nimh.nih.gov
, dicom_hdr - Prints selected information from the DICOM file.
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