image thumbnail

updated 1 month ago

DICOM to NIfTI converter by Xiangrui Li

dicm2nii.m converts dicom files into nifti files. (dicom, nifti, siemens)

dicm2nii(src, dataFolder, varargin)

dicm_dict(vendor, flds)

dicm_hdr(fname, dict, iFrames)

image thumbnail

updated 3 months ago

Magnitude-Sorted List, Multi-Clustering Phase Unwrapping Algorithm by Florian Maier

Robust Phase Unwrapping for MR Temperature Imaging (phase unwrapping, phase unwrap, mri)

image thumbnail

updated 4 months ago

MRiLab v1.2 by Fang Liu

A Numerical Simulation Platform for Magnetic Resonance Imaging (MRI) (medical imaging, medical, mri)

ADCRadial.m

AboutMRiLab(varargin)

About_MU(varargin)

image thumbnail

updated 4 months ago

IEV channel combination by Junmin

IEV represents an algorithm for local frequency mapping from multi-ch and multi-echo data (mri, swi, qsm)

ChComb_UsingIEV(LFS_fromEachCHatEachEcho,IEV_w)

FourierFilter_2D(PU, sigma,FOVx,FOVy,FOVz)

IEV_filtUsingGaussian(unwrap_phase,TE,sigma,FOVx, FOVy,FO...

image thumbnail

updated 4 months ago

Cross Section Isosurface by Evan

easily plot and color 3D data (3d, data exploration, figure)

CrossSectionIsosurface(density3D, varargin)

testCrossSectionIsosurface

image thumbnail

updated 5 months ago

MatrixUser v2.1.1 by Fang Liu

A Multi-functional, GUI-based Program for Image (Matrix) Processing and Analysis (image processing, image analysis, medical)

About_MU(varargin)

Flag=MU_load_matrix(matrixName, matrix, newWindowOpenFlag)

MU_3D_Render(varargin)

image thumbnail

updated 6 months ago

improj3 by Fang Liu

improj3 generates 3D projections from image stacks (image analysis, image processing, mip)

improj3(images)

image thumbnail

updated 6 months ago

immovie2 by Fang Liu

IMMOVIE2 make movie from multiframe superimposed images (image processing, immovie, movie)

immovie2(varargin)

example.m

image thumbnail

updated 7 months ago

Phase Unwrapping using Recursive Orthogonal Referring (PUROR) by Junmin

PUROR presents a fast phase unwrapping algorithm. (phase unwrapping, b0 mapping, qsm)

NoiseEstimation(complex_image)

PUROR2D( complex_image,mask4unwrap, mask4supp, mask4stack...

PUROR2D_doit(phase_original,mask_2D,mask_2D_h,debug_PUROR)

image thumbnail

updated 7 months ago

Anonymize Siemens rda-files by Paul Groot

Remove or modify metadata from native Siemens MRS files (mri, deidentification, pseudonimization)

anonrda( rdaFileIn, rdaFileOut, replacements, bVerbose, b...

image thumbnail

updated 7 months ago

Siemens DICOM sort and convert to NIfTI by Simon Robinson

Converts Siemens MRI DICOM data into NIfTI format, and/or anonymises and sorts into scan directories (dicom, nifti, mri)

centre_header(nii_hdr)

convert_2dto3d_func2(obj, eventdata, interleave_sort, rea...

convert_to_analyze_func(data)

image thumbnail

updated 7 months ago

Field-shift calculation without aliasing. by Job

Efficient forward Fourier-based calculation of the susceptibility-induced field shift in MRI (mri, magnetic susceptibili..., aliasing)

calculateFieldShift(X_dev, voxelSize)

demonstration.m

image thumbnail

updated 7 months ago

The Maximum Spacing Noise Estimation in Single-coil Background MRI Data by Tomasz Pieciak

Matlab implementations of the maximum spacing noise estimators (mri, noise estimation, maximum spacing estim...)

Aja_first_order_moment(data, window, bins)

Aja_first_order_moment_granularity(data, window, granular...

Aja_second_order_moment(data, window, bins)

image thumbnail

updated 7 months ago

Multiecho enhancement for 2D/3D (N-D) images by Luke Xie

Enhances images using a weighted sum or MEFIC. (2d, 3d, grayscale)

img2=multiecho_enhance(img,str,weights)

image thumbnail

updated 10 months ago

Joint Anisotropic Wiener filter for Diffusion Weighted MRI by Antonio Tristán Vega

Denoises Diffusion Weighted MRI volumes corrupted with stationary Rician noise (mri, dtmri, diffusion weighted mr...)

jaLMMSEDWI( DWInoisy, Grads, sigma, varargin )

test_jaLMMSE.m

image thumbnail

updated 11 months ago

Fast and robust Nonlocal Means Denoising by Antonio Tristán Vega

Efficient implementation of the non-local means for both Rician and Gaussian noise. (mri, denoising, nonlocal means)

FastNonLocalMeans3D.m

image thumbnail

updated 11 months ago

simulate motion in Cartesian MRI by Michael Völker

Simulates Point Spread Function (PSF) and k-space data for motion in Cartesian sequences. (mri, imaging)

cmap=morgenstemning(n,varargin)

getMotion( t, varargin )

getReorderLinesCartesian( varargin )

image thumbnail

updated 1 year ago

Fourier Decomposition Demo by Job

Visualizes how an image can be decomposed (and reconstructed) in 2D sinusoidal waves. (fourier transform, image reconstruction, mri)

FourierImageDecomposition.m

image thumbnail

updated 1 year ago

Reading Philips MR Physiolgy logfiles by Paul Groot

ReadPhilipsScanPhysLog.m reads Philips scanphyslog files, which are created by Philips MRI scanners. (mri, philips, physiological)

ReadPhilipsScanPhysLog(filename, channels, skipprep)

image thumbnail

updated 1 year ago

Brain Message v 1.0 to write secret messages into fMRI by Vanessa

Write secret messages in fMRI data to be uncovered with independent component analysis (fmri, ica, independent component...)

BrainMessage(message,outname)

image thumbnail

updated 1 year ago

MRI Partial Fourier reconstruction with POCS by Michael Völker

Fast and robust reconstruction of Cartesian partial Fourier MRI data with POCS (partial fourier, pocs, mri)

pocs( ksp, iter, watchProgress )

pocs_example.m

image thumbnail

updated almost 2 years ago

Interactive DICOM 3D Viewer by Eric Johnston

Viewer allows user to look through cross sections of a dicom image set. (dcm, dicom, 3d viewer)

Interactive DICOM 3D Viewer

dcm3DViewer

image thumbnail

updated 2 years ago

Dynamic non-local means (DNLM) for denoising of dynamic medical image sequences by Yaniv

Effective and robust denoising for 4D medical images (e.g. DCE-MRI, fMRI, dynamic PET) (noise, denoising, medical images)

dnlm.m

estimate_noise_dwt(img, Wname)

image thumbnail

updated 2 years ago

RAPID: a Routine Assurance Pipeline for Imaging of Diffusion by Silvia

uses diffusion MRI data for Quality Assurance of diffusion acquisitions (diffusion, mri, quality assurance)

DTI_bootstrap.m

DTI_metrics.m

DTI_metrics_2.m

image thumbnail

updated 2 years ago

LMMSE filter for Rician MRI data by SANTIAGO AJA-FERNANDEZ

A filtering scheme for denoising MR data assuming an underlying Rician model. (mri, noise, denoising)

I_est=MRI_lmmse(Im,Ws,varargin)

image thumbnail

updated 2 years ago

Parallel MRI noisy phantom simulator by SANTIAGO AJA-FERNANDEZ

Simulator of noisy parallel acquisition MR data (GRAPPA and SENSE included) (magnetic resonance, noise, parallel imaging)

Wx=coef_x(coef,tasa,N,mode,full)

[Im]=k2x(ik,method)

[Im]=sos(iX)

image thumbnail

updated 2 years ago

Heart perfussion MRI phantom simulator by SANTIAGO AJA-FERNANDEZ

To create a MR perfusion phantom of the heart with basic artifacts and noise. (perfusion, phantom, mri)

S0n=distort_sg(S0,sigma,blur,field, Knoise,ncorr,coils)

Sbig=periodic_sg(S0)

Sbig=periodic_sg(S0)

image thumbnail

updated 2 years ago

Noise estimators for MRI data Toolbox by SANTIAGO AJA-FERNANDEZ

Several methods to automatically estimate the level of noise in single- and multiple-coil MRI (noise estimation, mri, image processing)

CV=cvlocal(I,Ws,inses)

M=localMAD(I,Wn)

Vl=localvar3D_mask(I,mask,Ws,inses)

image thumbnail

updated 2 years ago

Function for Viewing MRI Slices by Aras

Allows the viewing of slices of MRI data in the NIFTI format. (nifti, mri, slice)

splic(x,y,z,t)

image thumbnail

updated almost 3 years ago

ct3 - A Simple Mousewheel-based 3D Image Browser for Medical Images by Tripp

A minimalist 3D Medical Image browser. Use the mousewheel to scroll between slices in all 3 planes. (medical imaging, 3d browser, mousewheel)

ct3(im,w)

image thumbnail

updated 3 years ago

Field Mapping Toolbox by Simon Robinson

Methods for B0 Mapping with Multi-Channel RF Coils in MRI (Robinson and Jovicich, MRM, 2011) (mri, field mapping, multichannel rf coils)

Y=pad(varargin)

[x,y,z,v]=find3(arr);

centre_and_save_nii(image_nii, filename, pixdim)

image thumbnail

updated 3 years ago

Visualize 3D volumetric image data such as MRI images in Matlab by Binlin Wu

Display 3D volumetric data such as MRI images dynamiclly. Click on an image to change the position. (biotech, image processing, 3d images)

mriplot.m

image thumbnail

updated 3 years ago

Sort DICOM CD images by subject and scan names by Gang Wang

Sort DICOM CD images by subject and scan names. (dicom, cd, sort)

sort_one_cd(realtopdir,dest_folder_str)

image thumbnail

updated 3 years ago

3D CT/MRI images interactive sliding viewer by Gang Wang

An interactive tool for users to browse through sagittal, axial and coronal views of CT/MRI images. (3d medical image, ct, mri)

moveitX(h,A)

moveitY(h,A)

moveitZ(h,A)

image thumbnail

updated 3 years ago

3D image slice viewer by Deshan Yang

A 3D volumetric data slice viewer for viewing 3D data in different orientations. (image processing, gui, ct)

contourd(varargin)

dim=mysize(m)

plot_contourd(contours,varargin)

image thumbnail

updated 3 years ago

create_mosaic.m by Simon Robinson

create_mosiac.m - Create tiled "mosaic" images from volumes (mri, fmri, nifti)

centre_and_save_nii(image_nii, filename, pixdim)

centre_header(nii_hdr)

load_nii(filename, img_idx, dim5_idx, dim6_idx, dim7_idx,...

image thumbnail

updated 3 years ago

Viewer3D by Dirk-Jan Kroon

MIP, Color, Slice and Shaded 3D (shearwarp) Volume Rendering, interactive 3D view/measurement GUI (volume render, volume rendering, mip)

B=SnakeInternalForceMatrix2D(nPoints,alpha,beta,gamma)

B=SnakeInternalForceMatrix3D(FV,alpha,beta,gamma)

ErrorData3D(varargin)

image thumbnail

updated 3 years ago

Noise estimation from rician noise corrupted images by Jeny Rajan

This program can be used for estimating noise from an image corrupted with rician noise (eg: MRI) (noise estimation, noise variance, rician noise)

[nsigma]=Nsigmaest1(Nimg)

[nsigma]=Nsigmaest2(Nimg)

polyexp(x)

image thumbnail

updated 4 years ago

MRI slice viewer by Ronald Ouwerkerk

This function will draw multiple MR images in 3D space using DICOM header information (mri, 3d visualization, image processing)

DrawImageSlice3D( dicom_filename, fighandle, transparen...

image thumbnail

updated 4 years ago

multimodality non-rigid demon algorithm image registration by Dirk-Jan Kroon

non-rigid 2D and 3D image registration with demon (fluid) algorithm, extended with modality transf. (transforms, nonrigid image regist..., nonrigid)

A=imresize3d(V,scale,tsize,ntype,npad)

E=strain(Ux,Uy,Uz)

I3=movepixels(I1,Tx,Ty,Tz,mode)

image thumbnail

updated 4 years ago

xjView, viewing program for SPM2 and SPM5 by Xu Cui

p-value slider, single-click to get anatomical description (imaging, mri, spm)

xjview(varargin)

image thumbnail

updated 4 years ago

MRI 3D interactive viwer by Ibraheem Al-Dhamari

Read and View ANALYZE images format. (mri, fmri, analyze)

MRIViewerB(varargin)

image thumbnail

updated almost 5 years ago

Bias Field Corrected Fuzzy C-Means by Dirk-Jan Kroon

Estimates the illumination artifact in 2D (color) and 3D CT and MRI and segments into classes. (bias field, biasfield, segmentation)

I=imgaussian(I,sigma,siz)

[B,U]=BCFCM2D(Y,v,Options)

BCFCM3D.m

image thumbnail

updated almost 5 years ago

Extended version of FT.m func of file ID: #21130 by Alper Yaman

This function is the new version of FT.m function of package ID: #21130. (dti, mri, fiber)

fibers=FT(FA,VectorF,Roi,parameters)

image thumbnail

updated 5 years ago

Transform matrix between two dicom image coordinates by Alper Yaman

This code calculates the transform matrix between two image coordinates. (image processing, mri, dicom)

GetTransformMatrix(info1, info2)

image thumbnail

updated 5 years ago

Joint Estimation for EPI functional MRI using Harmonic Retrieval by Hien

Implementation of harmonic retrieval for MRI image reconstruction (mri, image reconstruction, harmonic retrieval)

SNR(in, est)

Z=Matrix_z(z,N,M)

[x,obj_hat]=simdata_T2star(obj,we,N1,N2,M1,M2,d1,d2,delta...

image thumbnail

updated 6 years ago

DTI and Fiber Tracking by Dirk-Jan Kroon

Diffusion MRI (DTI), calculates FA, ADC, Vector Field, and will track and visualize neural tracts. (image analysis, dti, diffusion)

[ADC,FA,VectorF,DifT]=DTI(DTIdata,parameters)

[info] =gipl_read_header(fname)

fibers=FT(FA,VectorF,Roi,parameters)

image thumbnail

updated almost 7 years ago

Varian MRI FDF reader by Shanrong Zhang

Open and display Varian FDF image. (application, varian, fdf)

fdf

image thumbnail

updated 7 years ago

Interpolation with Reverse Diffusion by Olivier Salvado

Partial volume correction method using reverse diffusion interpolation (enhancement, interpolation, diffusion)

PVcorr2D.m

go1.m

uigetfiles.m

image thumbnail

updated 9 years ago

Pixelsurfer by Soren Christensen

Framework for pixel surfing time series data. Ideal for MR and PET tracer data. (data exploration, image pixel coordinat..., timeseries)

pixelsurfer(varargin)

Contact us