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AppleSiliconForNeuroimaging
Review the challenges and potential of ARM-based Apple Silicon macOS for brain imaging researchsurf-ice
GLSL surface rendering source code. Compiled versions available from NITRC. Loads 3DS, CTM, DXF, FreeSurfer, GII (GIfTI), GTS, LWO2, MS3D, MZ3, NV (BrainNetViewer), OBJ, OFF, PLY, STL, VTK. Tractography formats include BFloat, PDB, TCK, TRK, and VTK. Also NIfTI format voxelwise images.nii2mesh
Convert NIfTI volume to triangulated mesh using marching cubesMRIcron
Simple medical imaging visualization tool designed for NIfTI images. Includes dcm2nii for conversion of DICOM, Philips, and other proprietary formats.Fast-Quadric-Mesh-Simplification-Pascal-
Mesh triangle reduction using quadrics (for Delphi, Lazarus and Pascal)MRIcroGL10_OLD
DEPRECATED development has moved to https://github.com/rordenlab/MRIcroGLClinical
Clinical Toolbox for SPM (https://www.nitrc.org/projects/clinicaltbx/)NiiStat
NiiStat is a set of Matlab scripts for analyzing neuroimaging data from clinical populationsMetal-Demos
Examples of Apple's Metal API using Lazarus and Ryan Joseph's lazmetalcontrolvx
Simple Volume Rendererfsl_sub
parallel FSL processing without requiring SGEnii_preprocess
nii_preprocess adapted for LARC and ABC studies at UofSCMRIcro
macOS Xcode GLSL Volume Render for NIfTI, Bio-Rad Pic, NRRD, Philips, ITK MetaImage, AFNI, Freesurfer, DICOM images.OpenGLCoreTutorials
Cross-platform (Linux, Mac and Windows) OpenGL projects using Core specificationBru2Nii
Bruker ParaVision to NIfTI conversiondcm_qa
DICOM to NIfTI/BIDS validation scriptplyview
Demo OpenGL Core GLSL viewer for PLY or OBJ meshes using lazarussimd_crc
Showcase Chromium SIMD CRCNotarizeFPC
Notarizing FreePascal Command Line Toolssimplifyjs
Live three.js mesh simplification demo https://neurolabusc.github.io/simplifyjs/surfice_atlas
Convert NIfTI-format atlases to Surface MZ3 meshesgpu_test
Test FSL GPU acceleration (bedpost, eddy, probtrackx)niiTools
Utilities for brain imagingPyDog
Python Difference of Gaussian (DoG) edge finding demonstration MRI datasimd
Evaluating Single Instruction Multiple data (SIMD) with modern compilers, simple mathematics and modern memory constrained computers.VolumeRenderingData
Sample datasets for tools like MRIcroGL https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPageDistanceFields
Rapid thickness estimates for imagesPart
dcm_qa_cs_dl
DICOM compressed sensing and deep learning validation datasetezANOVA
[ezANOVA for simple Analysis of Variance](http://people.cas.sc.edu/rorden/ezanova/index.html)zlib-bench-python
Test of compression accelerationdcm_qa_philips
DICOM to NIfTI/BIDS validation script for Philips DICOMsniivue-images
Sample NIfTI images for demonstrating and validating NiiVuefsl_bianca
Notes on using [FSL's BIANCA](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BIANCA)mri-qa
Magnetic Resonance Imaging Quality Assurance Matlab scriptsdcm_qa_uih
DICOM validation dataset for United Imaging Healthcare ("UIH") MRI scannerspigz-bench
Test of parallel compression acceleration for Unix (MacOS and Linux)niiSmooth
Fast Gaussian blur for neuroimaging datasetsdcm_qa_agfa
AGFA Impax PACS re-assignment of DICOM Private Elementsdcm_qa_ge
DICOM to NIfTI/BIDS validation script for data from GE MRIopen_source_eegecgemg
Do-It-Yourself Electrophysiology (Arduino, Matlab, Processing)pigz-bench-python
Test of parallel compression acceleration. (deprecated, please go to https://github.com/zlib-ng/pigzbench)Metal
Metal compute shadersdcm_qa_trt
GE TotalReadoutTime validation datasetPython27-for-Lazarus
Fork of Python-for-Lazarus supports legacy Python 2.7 on Windows/Linux/macOSblog
Lab notes https://neurolabusc.github.io/blog/.dcm_qa_xa30
DICOM to NIfTI/BIDS validation script for Siemens XA30Cancel
Simple continuous measures for assessing spatial neglectmri-contrast
Matlab scripts to illustrate how MRI parameters (repetition and echo time) impact signalbiquad-filter
Filter to attenuate chosen frequencies, visual Fast Fourier Transform (FFT) shows roll-offcoreg_qa
Methods for generating quality assurance images for 3D coregistration of brain imagesLewinerMarchingCubes
AFNI marching cubesStimSync
USB device for digital and analog inputs and outputsdcm_qa_fmap
DICOM to NIfTI/BIDS validation script for direct fieldmapsdcm2niiXL
Accelerated dcm2niix DICOM to NIfTI for extra large datasetsdcm_qa_pdt2
DICOM to NIfTI/BIDS validation script for PDT2 sequencesspatial-processing
Interactive programs showing spatial transforms (Otsu, blur, affine, etc.) and consequences of interpolation.dcm_qa_philips_asl_enh
Philips enhanced DICOM to NIfTI/BIDS arterial spin labeling validation scriptdcm_qa_philips_enh
Philips MRI data exported as both enhanced and classic DICOMELEcro
A simple viewer for electrophysiological data (EMG, ERP, EEG)nii2meshCPP
Convert NIfTI volume to triangulated mesh using marching cubes (Obsolete C++, see C implementation)Compact-Julich-Brain-Atlas
Scripts to convert the huge Julich-Brain-Atlas for efficient displayc-ray
A classic parallel threading benchmarkMRIcroGL_AFNI
Beta release of MRIcroGL with improved AFNI supportFPCintrinsics
Using SIMD Single Instruction/Multiple Data (SSE and Neon) Intrinsics in FreePascaldcm_qa_asl
DICOM to NIfTI/BIDS arterial spin labeling validation scriptNotarizeC
Notarizing C Command Line Tools for MacOStgzProcess
Use dcm2niix to convert and organize Siemens MRI datadcm_qa_canon
DICOM to NIfTI/BIDS validation script for data from Canon MRIneurolabusc.github.io
Web-based surface renderingMeshFormatsJS
JavaScript testing for popular neuroimaging mesh formatsmri_buttons
MRI-compatible buttons (https://crnl.readthedocs.io/diy_fmri/index.html)ComputeShaderWebGL
WebGL2 Texture3D compute shaders with live view https://neurolabusc.github.io/ComputeShaderWebGL/crnl
Chris Rorden's Neuropsychology Lab Web Pages https://crnl.readthedocs.io/oscilloscope
Wired or blue-tooth oscilloscope using Teensy or Arduino (Processing, Matlab, Xcode, Lazarus)dcm_qa_philips_dwi
DICOM to NIfTI/BIDS Philips diffusion weighted imaging validation scriptLove Open Source and this site? Check out how you can help us