Generate synthetic fMRI data by Jeremy Manning

This program is useful for debugging fMRI analyses and models. (nifti, brain, data)

generate_data(meta,X,SNR,TR,sim_hemodynamics,outfile,vararg...

make_nii(varargin)

save_nii(nii, fileprefix, old_RGB)

DICOM Example Files by Jeff Mather

Example DICOM files containing MR images of the brain. (brain, dicom, dicomread)

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)

2d and 3d brain plots by Jeremy Manning

Quickly and easily create 2d and 3d plots of fMRI data. (fmri, pcolor, 2d)

PATCH_3Darray(varargin)

getTightSubplotHandles(FIG_MARGIN,ROW_MARGIN,COLUMN_MARGIN,...

plot_brain2d(x,meta,nrow,ncol,dim,c,s)

Intensity normalization of Brain volume by Alessandro Crimi

Intensity normalization of Brain volume given a reference volume (nifti, intensity normalizati..., brain)

emgm(X, init, prob_prior)

get_nii_frame(fileprefix)

hellier_hist_normalization_gmm( file_name_template, file_na...

Active contours driven by local Gaussian distribution fitting energy by li

This Matlab code implements a segmentation method using local Gaussian distribution fitting energy. (image segmentation, segmentation, level set)

evolution_LGD(Img,u,epsilon,Ksigma,KONE,KI,KI2,mu,nu,lambda...

Demo_LGD_1.m

Demo_LGD_2.m

Estimating Time-varying Neural Interactions by Hideaki Shimazaki

Matlab code for estimating time-varying interactions of neurons from spike data. (statistics, mathematics, optimization)

BayesFactor(model,cell_id)

BayesFactor(model,cell_id)

CompSync(raw,D,r)

Electrocorticography / intracranial EEG visualizer by Matthew Davidson

This is a tool for plotting iEEG/ECog data on a brain. (ieeg, ecog, visualization)

ft_group_ieeg_elec_plot(varargin)

keeponly_electrodes(elec, wh)

plot_brain(surf_brain, viewpoint, varargin)

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)

IPN_voxelGraph by Xi-Nian Zuo

Functions to Generate Large Correlation Matrix and Sparse Matrix of Huge Graph. (correlation, brain, connectome)

IPN_calLCAM(data, thresh, nblock, connType)

IPN_fastCorr(X, Y)

MRI Brain Segmentation by Robert Bemis

Neuroimaging Case Study for seminars and webinars. (brain, 3d segmentation, segmentation)

StepThru(mfile,ws)

UpdateSliceOMatic(X,hSlico)

[x,y]=limits(a)

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)

IPN tools for Test-Retest Reliability Analysis by Xi-Nian Zuo

This is one part of my IPN toolbox, aiming at the reliability analysis of neuroimaging meaures. (probability, icc, ccc)

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)

BrainMaps Analyze by Shawn Mikula

BrainMaps Analyze is a powerful tool for applying image analysis routines to BrainMaps.org high reso (medical, brain, image processing)

bmanalyze( varargin )

bmanalyzeGetPaths( varargin )

bmanalyzeInfo( varargin )