Discover neurolabusc/DistanceFields Open Source project

Convert NIfTI volume to triangulated mesh using marching cubes

102

nii2mesh

MRIcron

Simple medical imaging visualization tool designed for NIfTI images. Includes dcm2nii for conversion of DICOM, Philips, and other proprietary formats.

Mesh triangle reduction using quadrics (for Delphi, Lazarus and Pascal)

Fast-Quadric-Mesh-Simplification-Pascal-

DEPRECATED development has moved to https://github.com/rordenlab/MRIcroGL

MRIcroGL10_OLD

Clinical Toolbox for SPM (https://www.nitrc.org/projects/clinicaltbx/)

Clinical

NiiStat is a set of Matlab scripts for analyzing neuroimaging data from clinical populations

NiiStat

Examples of Apple's Metal API using Lazarus and Ryan Joseph's lazmetalcontrol

Metal-Demos

Simple Volume Renderer

parallel FSL processing without requiring SGE

fsl_sub

nii_preprocess adapted for LARC and ABC studies at UofSC

nii_preprocess

macOS Xcode GLSL Volume Render for NIfTI, Bio-Rad Pic, NRRD, Philips, ITK MetaImage, AFNI, Freesurfer, DICOM images.

MRIcro

Cross-platform (Linux, Mac and Windows) OpenGL projects using Core specification

OpenGLCoreTutorials

Bruker ParaVision to NIfTI conversion

Bru2Nii

DICOM to NIfTI/BIDS validation script

dcm_qa

Demo OpenGL Core GLSL viewer for PLY or OBJ meshes using lazarus

plyview

Showcase Chromium SIMD CRC

simd_crc

NotarizeFPC

Notarizing FreePascal Command Line Tools

Live three.js mesh simplification demo https://neurolabusc.github.io/simplifyjs/

simplifyjs

JavaScript

surfice_atlas

Convert NIfTI-format atlases to Surface MZ3 meshes

Test FSL GPU acceleration (bedpost, eddy, probtrackx)

gpu_test

Utilities for brain imaging

niiTools

Python Difference of Gaussian (DoG) edge finding demonstration MRI data

PyDog

Python

simd

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:MainPage

Part

DICOM compressed sensing and deep learning validation dataset

dcm_qa_cs_dl

[ezANOVA for simple Analysis of Variance](http://people.cas.sc.edu/rorden/ezanova/index.html)

ezANOVA

DICOM to NIfTI/BIDS validation script

dcm_qa_nih

Test of compression acceleration

zlib-bench-python

Python

dcm_qa_philips

DICOM to NIfTI/BIDS validation script for Philips DICOMs

Sample NIfTI images for demonstrating and validating NiiVue

niivue-images

fsl_bianca

Notes on using [FSL's BIANCA](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BIANCA)

Magnetic Resonance Imaging Quality Assurance Matlab scripts

mri-qa

DICOM validation dataset for United Imaging Healthcare ("UIH") MRI scanners

dcm_qa_uih

Test of parallel compression acceleration for Unix (MacOS and Linux)

pigz-bench

Fast Gaussian blur for neuroimaging datasets

niiSmooth

AGFA Impax PACS re-assignment of DICOM Private Elements

dcm_qa_agfa

dcm_qa_ge

DICOM to NIfTI/BIDS validation script for data from GE MRI

Do-It-Yourself Electrophysiology (Arduino, Matlab, Processing)

open_source_eegecgemg

Test of parallel compression acceleration. (deprecated, please go to https://github.com/zlib-ng/pigzbench)

pigz-bench-python

Python

Metal

Metal compute shaders

Swift

dcm_qa_trt

GE TotalReadoutTime validation dataset

Fork of Python-for-Lazarus supports legacy Python 2.7 on Windows/Linux/macOS

Python27-for-Lazarus

Lab notes https://neurolabusc.github.io/blog/.

blog

dcm_qa_xa30

DICOM to NIfTI/BIDS validation script for Siemens XA30

Simple continuous measures for assessing spatial neglect

Cancel

Matlab scripts to illustrate how MRI parameters (repetition and echo time) impact signal

mri-contrast

Filter to attenuate chosen frequencies, visual Fast Fourier Transform (FFT) shows roll-off

biquad-filter

Methods for generating quality assurance images for 3D coregistration of brain images

coreg_qa

LewinerMarchingCubes

AFNI marching cubes

StimSync

USB device for digital and analog inputs and outputs

DICOM to NIfTI/BIDS validation script for direct fieldmaps

dcm_qa_fmap

Accelerated dcm2niix DICOM to NIfTI for extra large datasets

dcm2niiXL

DICOM to NIfTI/BIDS validation script for PDT2 sequences

dcm_qa_pdt2

Interactive programs showing spatial transforms (Otsu, blur, affine, etc.) and consequences of interpolation.

spatial-processing

Philips enhanced DICOM to NIfTI/BIDS arterial spin labeling validation script

dcm_qa_philips_asl_enh

Philips MRI data exported as both enhanced and classic DICOM

dcm_qa_philips_enh

A simple viewer for electrophysiological data (EMG, ERP, EEG)

ELEcro

Convert NIfTI volume to triangulated mesh using marching cubes (Obsolete C++, see C implementation)

nii2meshCPP

Scripts to convert the huge Julich-Brain-Atlas for efficient display

Compact-Julich-Brain-Atlas

A classic parallel threading benchmark

c-ray

MRIcroGL_AFNI

Beta release of MRIcroGL with improved AFNI support

FPCintrinsics

Using SIMD Single Instruction/Multiple Data (SSE and Neon) Intrinsics in FreePascal

dcm_qa_asl

DICOM to NIfTI/BIDS arterial spin labeling validation script

Notarizing C Command Line Tools for MacOS

NotarizeC

Use dcm2niix to convert and organize Siemens MRI data

tgzProcess

DICOM to NIfTI/BIDS validation script for data from Canon MRI

dcm_qa_canon

Web-based surface rendering

neurolabusc.github.io

JavaScript

MeshFormatsJS

JavaScript testing for popular neuroimaging mesh formats

mri_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/

JavaScript

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)

DICOM to NIfTI/BIDS Philips diffusion weighted imaging validation script

dcm_qa_philips_dwi