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)

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

Interactive DICOM 3D Viewer by Eric Johnston

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

Interactive DICOM 3D Viewer

dcm3DViewer

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)

MRI field-shift calculation with virtual Zero-Padding by Job

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

FBFC_CC_no_padding(X_dev)

FBFC_CC_vZP(X_dev, degree)

FBFC_KF_vZP(X_dev, degree)

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

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)

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)

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)

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)

Brain Mask by Ben Duffy

Automatic brain masking for MRI volumes; (image processing, mri, mask)

brainmask(volume)

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)

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)

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)

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. (volumetric, 3d images, biotech)

mriplot.m

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)

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, image processing)

moveitX(h,A)

moveitY(h,A)

moveitZ(h,A)

3D image slice viewer by Deshan Yang

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

contourd(varargin)

dim=mysize(m)

plot_contourd(contours,varargin)

create_mosaic.m by Simon Robinson

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

centre_and_save_nii(image_nii, filename, pixdim)

centre_header(nii_hdr)

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

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, siemens, mri)

centre_header(nii_hdr)

convert_2dto3d_func2(obj, eventdata, interleave_sort, readf...

convert_to_analyze_func(data)

Viewer3D by Dirk-Jan Kroon

MIP, Color, Slice and Shaded 3D (shearwarp) Volume Rendering, interactive 3D view/measurement GUI (3d, dicom, mip)

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

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

ErrorData3D(varargin)

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)

MRI slice viewer by Ronald Ouwerkerk

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

DrawImageSlice3D( dicom_filename, fighandle, transparency...

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. (2d, 3d, registration)

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

E=strain(Ux,Uy,Uz)

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

xjView, viewing program for SPM2 and SPM5 by Xu Cui

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

xjview(varargin)

MRI 3D interactive viwer by Ibraheem Al-Dhamari

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

MRIViewerB(varargin)

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 estimation, illumination, segmentation)

I=imgaussian(I,sigma,siz)

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

BCFCM3D.m

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)

Transform matrix between two dicom image coordinates by Alper Yaman

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

GetTransformMatrix(info1, info2)

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,delta1,...

DTI and Fiber Tracking by Dirk-Jan Kroon

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

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

[info] =gipl_read_header(fname)

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

Varian MRI FDF reader by Shanrong Zhang

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

fdf

Interpolation with Reverse Diffusion by Olivier Salvado

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

PVcorr2D(Ir,ratio,option);

go1.m

uigetfiles.m

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)

readanalyze.m by Colin Humphries

Read MRI files in the Analyze format. (data import, data export, fmri)

readanalyze(filename)

MRI Analyze tools by Darren Weber

Read/View Analyze data format (MRI). (analyze, mri, medical)

mriphantom by Ronald Ouwerkerk

Simulation of raw MRI data from k-space coordinates using the Shepp and Logan head phantom function. (medical, mri, kspace)

mriphantom(kx,ky)

pifft by Edward Brian Welch

Homodyne reconstruciton of partial MRI k-space (Spatial Frequency) data (reconstruction, partial fourier, fft)

pifft(pksp)

MRIotl by Mark Hasegawa-Johnson

MRIotl -- a tool for editing MRI image files (medical, mri, zoom)

EditOtl(action, arg)

LoadImageFcn( ACTION, TAGBASE, LEVEL, ARGUMENT )

MRIotl(directory)