SPM Extensions
http://www.fil.ion.ucl.ac.uk/software/spm/ext/
Statistical Parametric Mapping Extensions
nichols@umich.edu (Tom Nichols)
http://blogs.law.harvard.edu/tech/rss
1440

AQuA
http://www.ibime.upv.es/mi/
lnjuanj@gmail.com (Antonios Antoniou and Juan J. Lull)
Toolbox for spm5
AQuA is a tool that helps you in the assessment process for the quality of the acquired fMRI data, identifying images with movement and other artefacts, so that they do not compromise the experimental analysis.

AAL  Anatomical Automatic Labeling
http://www.gin.cnrs.fr/spip.php?article217
aalgin@cyceron.fr (Cyceron)
Toolbox for spm99,spm2,spm5,spm8
Automated parcellation method, as described in TzourioMazoyer et al. NI 2002.

ACID  Artefact correction in diffusion MRI
http://www.diffusiontools.com/
siawoosh.mohammadi@ucl.ac.uk (Siawoosh Mohammadi)
Toolbox for spm8
The Artefact correction in diffusion MRI (ACID) toolbox is an academic software toolkit for preprocessing of diffusion MRI data, estimation of DTI indices and normalisation of DTI index maps, which fully integrates into the batch system of SPM8.

ALVIN  Automatic Lateral Ventricle delIneatioN
http://sites.google.com/site/mrilateralventricle/
matthew.kempton@kcl.ac.uk (Matthew Kempton)
Toolbox for spm8
Segmentation of the lateral ventricles validated in infants, adults and patients with Alzheimer's disease. Works with both T1 and T2 images.

ArtRepair  Artifact Repair toolbox
http://cibsr.stanford.edu/tools/humanbrainproject/artrepairsoftware.html
mazaika@stanford.edu (Paul Mazaika)
Toolbox for spm2,spm5,spm8
Special methods to improve the fMRI analysis of high motion pediatric and clinical subjects. The methods correct for large motions, and automatically detect and remove artifact noise in the data. Viewing tools allow quality checking at every step in the analysis.

AMAT: A metaanalysis toolbox
http://www.antoniahamilton.com/amat.html
antonia.hamilton@nottingham.ac.uk (Antonia Hamilton)
Toolbox for spm2
AMAT is a matlab program which lets you search through the coordinates reported in lots of fMRI papers. It is designed to answer the frequently asked question: what the *?%! does that bit do?

AnalyzeMovie  AVI movies from Analyze images
http://www.sph.umich.edu/nistat/AnalyzeMovie.tar
rcwelsh@med.umich.edu (Robert Welsh)
Toolbox for spm99
Create AVI movies from Analyze images, of axial, coronal, sagittal or ortho slices. Requires Matlab6 or greater.

Anatomy  SPM Anatomy toolbox
http://www.fzjuelich.de/inm/inm1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html
S.Eickhoff@fzjuelich.de (Simon Eickhoff)
Toolbox for spm99,spm2,spm5,spm8
This toolbox integrates probabilistic cytoarchitectonic maps derived from human postmortem studies into the SPM environment and provides a wide range of different approaches to analyse structure / function correlations.

aslm  a slightly modified aslmodule
http://aslm.sourceforge.net
homan@puk.unibe.ch (Philipp Homan)
Toolbox for spm8
aslm is an object orientated toolbox for common tasks associated with the analysis of arterial spin labeling (ASL) and other MRI data.

ASLtbx
http://www.cfn.upenn.edu/~zewang/ASLtbx.php
zewang@mail.med.upenn.edu (Ze Wang)
Toolbox for spm2,spm5,spm8
ASLtbx is a Matlab and SPM based toolkit for processing arterial spin labeling (ASL) perfusion MRI data. It's basically a collection of a bunch of batch scripts. I'm currently only distributing the SPM5based version, but the SPM2(or 8)based version can be obtained through email. The function for quantifying cerebral blood flow should be SPM independent except the image reading and writing functions from SPM.

at4fmri  adaptive thresholding of fMRI maps
http://sourceforge.net/projects/at4fmri/
cyril.pernet@ed.ac.uk (Chris Filo Gorgolewski and Cyril Pernet)
Toolbox for spm8
Allow to obtain a threshold for cluster FDR  the method fits a GammaGaussian mixture model to the SPMT and finds the optimal threshold (crossing between noise and activation). Optionally write the thresholded maps.

aws4SPM
http://www.wiasberlin.de/software/aws4SPM/
tabelow@wiasberlin.de (Devy Hoffmann and Karsten Tabelow)
Toolbox for spm2,spm5,spm8
Structural adaptive smoothing fMRI data as described in Tabelow et al. NI (2006).

BrainNet Viewer
http://www.nitrc.org/projects/bnv/
mingruixia@gmail.com (Mingrui Xia)
Toolbox for
BrainNet Viewer is a brain network visualization tool, which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick, easy, and flexible way.

Brainnetome Atlas Viewer
http://atlas.brainnetome.org/
lingzhong.fan@gmail.com (Congying Chu, Lingzhong Fan, Tianzi Jiang)
Toolbox for
Brainnetome Atlas Viewer(v1.0) shows the anatomical connectivitybased parcellation results, including the maximum probabilistic maps, probabilistic maps and both the anatomical and functional connectivity patterns, which have been developed in Brainnetome Center(http://www.brainnetome.org/), CASIA. The atlas is based on the analysis of connectional architecture with in vivo multimodal MRI data during the last 3 years.

BredeQuery
http://neuro.imm.dtu.dk/wiki/BredeQuery
bw@imm.dtu.dk (Bartlomiej Wilkowski)
Toolbox for spm5
BredeQuery plugin for SPM5  enables coordinatebased metaanalytic search of related literature for brain regions directly from SPM5 environment. The coordinatebased search is performed using Finn Aarup Nielsen's Brede Database. Works with coordinates in Talairach and MNI space, MNItoTalairach transformations are available (Brett and Lancaster transformations). Moreover, query results can be exported automatically to the suitable bibliographic file format (BibTeX, Reference Manager, RefWorks, EndNote).

CCAfMRI
http://ccafmri.sourceforge.net/
magnus@imt.liu.se (Magnus Borga)
Toolbox for spm2,spm5
The CCAfMRI utilizes canonical correlation analysis in combination with the Balloon model and adaptive filtering of fMRI data to detect areas of brain activation. The CCAfMRI toolbox provides its own user interface and can also be used as stand alone scripts, e.g. for batch processing.

CLASS  Classifier Learning for Asymmetrically Small Samples
Contact email above
Ged.Ridgway@gmail.com (Ged Ridgway)
Toolbox for spm8
Multivariate kernelbased pattern classification using support vector machines (SVM) with a novel modification to obtain more balanced sensitivity and specificity on unbalanced datasets (i.e. those with very different numbers of cases in each group).

Clinical Toolbox
http://www.mccauslandcenter.sc.edu/CRNL/clinicaltoolbox
RORDEN@mailbox.sc.edu (Rorden, Bonilha, Fridriksson, Bender and Karnath)
Toolbox for spm8
Aids normalization of clinical scans, providing an easy way to include lesion cost function masking. Allows unified segmentationnormalization (USN) or traditional normalization. Includes custom age adjusted templates for CT/CAT scans and USN. Includes FLAIR template provided by the Glahn group.

Complexity
http://loftlab.org/index5.html
jiongwang@mednet.ucla.edu (Anitha Priya Krishnan, Jun Fang, Robert Smith, Danny JJ Wang )
Toolbox for spm8
Complexity is a toolkit used to analyze the complexity of resting state fMRI (rsfMRI) data. Preprocessing module is included to realize low pass filtering and linear detrending. Five methods, Approximate Entropy, Sample Entropy, Cross Approximate Entropy, Multiscale Sample Entropy and Wavelet MSE, are available to calculate the entropy. Matlab toolbox, "Tools for NIfTI and ANALYZE image", is needed.

conn  Functional Connectivity
http://web.mit.edu/swg/software.htm
alfnie@gmail.com (Alfonso NietoCastanon)
Toolbox for spm8
Performs functional connectivity analyses of fMRI data. Methods: Rest and task related connectivity. CompCor method for removing physiological and other confounds. Firstlevel univariate and multivariate regression and bivariate and semipartial correlation connectivity measures. Seedtovoxel and ROItoROI analyses. Second level random effect analyses. Gui and batch processing.

ConnExT  Connectivity Explorer Toolbox
http://www.lni.hc.unicamp.br/~beltramini
gcbeltramini@gmail.com (Guilherme Coco Beltramini)
Toolbox for spm8
Easy way to visually explore the signal time series and the functional connectivity map of fMRI data. There are various processing options that can be applied to the time series, and the effect is quickly seen. A seed region can also be chosen without difficulty for functional connectivity analysis, and the correlation coefficients map is instantaneously displayed. GUI and batch processing.

fMRI CPCA
http://www.nitrc.org/projects/fmricpca
toddswoodward@gmail.com (Todd Woodward)
Toolbox for
Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singularvalue decomposition of BOLD signal time series, and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time, using all other scans as baseline.

DAiSS
https://code.google.com/p/spmbeamformingtoolbox/
v.litvak@ucl.ac.uk (Vladimir Litvak)
Toolbox for spm12
SPM12 toolbox for Data Analysis in Source Space (beamforming, minimum norm and related methods), developed by collaboration of UCL, Oxford and other MEG centres.

DICOMCD Import
http://allserv.ugent.be/~pvdemael
Pieter.Vandemaele@UGENT.BE (Pieter Vandemaele)
Toolbox for spm5
This toolbox can import a Siemens DICOMCD (maybe other scanners too) to local storage without being confused about which dicom file belongs to which session. By analyzing the DICOMDIR file, all data is saved in dicom format, but split according to subject and sequence. It can also convert Siemens DICOMCD or imported data to NIFTI files without having to change directory multiple times.

Diffusion II  Postprocessing for diffusion weighted image series
http://sourceforge.net/projects/spmtools
volkmar.glauche@uniklinikfreiburg.de (Volkmar Glauche)
Toolbox for spm2,spm5,spm8
Postprocessing for diffusion weighted image series. Functionality includes movement correction for image time series, estimation of the diffusion tensor, computation of anisotropy indices and tensor decomposition.

Distance  Intersubject distances and permutation tests
http://groups.google.com/group/distancetoolbox
neurospin.distance@gmail.com (SÃ©bastien MÃ©riaux, Alexis Roche, Ferath Kherif, & Bertrand Thirion)
Toolbox for spm99,spm2
This toolbox features two independent modules: 1) tools for group homogeneity diagnosis using pairwise distances; 2) nonparametric randomeffect analysis using permutation tests. The permutation testing module is platformspecific: both Windows and 32bit Linux are currently supported. On other systems, a recompilation is needed (see instructions from the URL).

DPARSF Data Processing Assistant for RestingState fMRI
http://www.restfmri.net/forum/DPARSF
ycg.yan@gmail.com (ChaoGan Yan)
Toolbox for spm5,spm8
DPARSF is a convenient plugin software based on SPM and REST. You just need to arrange your DICOM files, and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data, FC, ReHo, ALFF and fALFF results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. You can use DPARSF to extract AAL or ROI time courses (or extract Gray Matter Volume of AAL regions, command line only) efficiently if you want to perform smallworld analysis. DPARSF basic edition is very easy to use, just click on buttons if you are not sure what it means, popup tips would tell you what you need to do. DPARSF advanced edition is much more flexible, you can use it to reorient your images interactively or define regions of interest interactively. You can skip or combine the processing steps in DPARSF advanced edition freely.

DRIFTER  An SPM toolbox for removing periodic noise in fMRI data
http://becs.aalto.fi/en/research/bayes/drifter/
arno.solin@aalto.fi (Arno Solin and Simo Sarkka)
Toolbox for spm8
The DRIFTER algorithm is a Bayesian model based method for eliminating physiological noise in fMRI data. The method can utilize external reference signals to identify the frequencies of cardiac and respirationinduced noise, and then eliminate them from the brain data. The toolbox can be operated both in graphical and batch mode.

EMS  Expectation Maximization Segmentation
http://www.medicalimagecomputing.com/downloads/ems.php
koen.vanleemput@hut.fi (Koen Van Leemput)
Toolbox for spm2
Fully automated modelbased segmentation of MR images of the brain. Uses MRFs to regularize segmentation and improve accuracy and can use multispectral data to segment lesions.

ExtractVals
http://wwwpersonal.umich.edu/~rcwelsh/ExtractVals.tar
rcwelsh@med.umich.edu (Robert Welsh)
Toolbox for spm2
Given a ROI binary mask image, this toolbox will extract values and report mean and variance.

FASL  Arterial Spin Labeling functional MRI data
http://web.eecs.umich.edu/~hernan/Public/Programs/
hernan@umich.edu (Luis Hernandez)
Toolbox for spm5,spm8
An interactive tool for analysis of arterial spin labeling functional MRI time series data. It includes preprocessing, physiological noise correction, OLS and GLS analysis, as well as quantification of perfusion.

FAST  fMRI artefact rejection and sleep scoring toolbox
http://www.montefiore.ulg.ac.be/~phillips/FAST.html
c.phillips@ulg.ac.be (Jessica Schrouff, Dorothee Coppieters & Christophe Phillips)
Toolbox for spm8,spm12
FAST is an EEG toolbox that can clean your EEG signal from the artefacts generated by the simultaneous acquisition of EEGfMRI data (both gradient and pulse artefacts). It is also tailored to handle (display, browsing, chunking, appending, etc.) of long continuous EEG recordings and to manually score sleep data.

fECM  Fast eigenvector centrality mapping
https://github.com/amwink/bias/tree/master/matlab/fastECM
a.m.wink@gmail.com (Alle Meije Wink)
Toolbox for spm5,spm8,spm12
This toolbox computes eigenvector centrality maps from 4D fMRI data sets in the NIfTI format  both .nii and .nii.gz extensions are supported. It uses the fast ECM algorithm, sidestepping the need to compute the whole voxeltovoxel connectivity matrix. The easiest way to control the algorithm is by calling the 'fegui' function which brings up a menu where fMRI data, masks and atlases can be selected. If an atlas of brain regions is used, each voxel of a region in the output map has the value of that region. Options can be set for number of iterations, writing out uniformly distributed maps (using ECM ranking) and normally distributed maps (after inverse transform sampling).

FDR  False Discovery Rate
http://wwwpersonal.umich.edu/~nichols/FDR/
nichols@umich.edu (Thomas Nichols)
Toolbox for spm99
Adds FDRcorrected pvalues and thresholds to SPM99 results page

FieldMap Toolbox
http://www.fil.ion.ucl.ac.uk/spm/toolbox/fieldmap/
chutton@fil.ion.ucl.ac.uk (Jesper Andersson & Chloe Hutton)
Toolbox for spm2
Toolbox for creating unwrapped field maps and unwarping EPI. Note that for SPM5 and above, the FieldMap Toolbox is part of the SPM distribution.

fieldmap_undistort  EPI distortion correction
http://imaging.mrccbu.cam.ac.uk/imaging/FmReference
rhodri.cusack@mrccbu.cam.ac.uk (Rhodri Cusack)
Toolbox for spm99
Uses a measured field map to undistort EPI images.

FieldTrip
http://fieldtrip.fcdonders.nl/
r.oostenveld@fcdonders.ru.nl (Robert Oostenveld)
Toolbox for spm8
FieldTrip is a MATLAB toolbox for MEG and EEG analysis. It includes algorithms for simple and advanced analysis of MEG and EEG data, such as timefrequency analysis, source reconstruction using dipoles, distributed sources and beamformers and nonparametric statistical testing.

fMRIPower
http://fmripower.org/
jeanette.mumford@gmail.com (Jeanette Mumford )
Toolbox for spm5,spm8
This tool is based on the work outlined in Mumford & Nichols, NeuroImage, 39(1):2618, 2008. Basically you load up your SPM.mat file (from a group analysis), choose the contrast you're interested in calculating power for, specify an ROI mask and sample size and the power calculation is done for you.

fOSA
http://www.ucl.ac.uk/medphys/research/borl/nirs/nirs/current_projects/funct_softdev/fosa
pkoh@medphys.ucl.ac.uk (Peck Hui Koh)
Toolbox for spm5
fOSA is a software package for the processing and analysis of functional neuroimaging data using Near Infrared Spectroscopy (NIRS).

Grocer
http://code.google.com/p/fmrigrocer/
zshtom@gmail.com,hengyi@gmail.com,husiyuan010@gmail.com (Senhua Zhu, Hengyi Rao and Siyuan Hu)
Toolbox for spm5,spm8
This toolbox contains many kinds of kits that you may be interested in for CBF(Cerebral Blood Flow) data analysis. This toolbox is run and tested on SPM8 with MATLAB 7.6.0 (R2008a) under Linux. Theoretically, most of the functions (except the first two menus which are specially designed for the Batch Editor of SPM8) of this toolbox should be compatible with SPM5 and should also work smoothly under the Windows OS. Read the manual in the package for more details.

HV
http://www.jungdiagnostics.de/eng/tools
service@jungdiagnostics.de (jung diagnostics GmbH)
Toolbox for spm8
HV is a SPM toolbox fully integrated into the SPM8 GUI to calculate hippocampal volumes based on 3D MPRAGE images.

IBASPM (Individual Brain Atlases using SPM)
http://www.thomaskoenig.ch/Lester/ibaspm.htm
lester@cneuro.edu.cu (Lester Melie Garcia and Yasser AlemanGomez)
Toolbox for spm2,spm5
A toolbox with GUI for segmenting automatically cerebral structures in MRI images in the individual anatomy space. Through this set of routines is able to compute the volume of gross anatomical structures. Other facilities are related to the computation of the SPAMs (Statistical Probability Anatomy Maps) and MaxPro (Maximum probability) maps that can be used in classification procedures. Also the computation of the gray matter, white matter, cerebral spinal fluid (CSF) volumes by hemisphere and total brain volume is affordable through this toolbox. All programs have been developed in the Neuroimaging Department, Cuban Neuroscience Center.

iBrain analysis toolbox
http://brain.org.au/iBrain/#ibrain_spmtools
d.abbott@brain.org.au (David Abbott)
Toolbox for spm2,spm5,spm8
The iBrain analysis toolbox for SPM is a free toolbox that provides an automated processing pipeline for various single or multisubject and/or multisession functional neuroimaging experiments. The pipeline includes image conversion from scannerspecific formats, preprocessing, statistical analysis, regionofinterest analysis, and display. It is possible to specify a complete analysis stream in advance (i.e. before any processing is actually performed). Analysis paradigms supported include blockdesign, eventrelated, simultaneous EEG/fMRI, and functional connectivity.

iBrain Laterality Toolbox
http://brain.org.au/iBrain/#ibrain_li
d.abbott@brain.org.au (David Abbott)
Toolbox for spm2,spm5,spm8
The iBrain Laterality Toolbox contains MATLAB scripts that implement an objective thresholdindependent assessment of whether the balance of activity between two regions of interest is typical or atypical, based on statistical comparison between an individual and a group of controls. The toolbox displays laterality index (LI) plots as a function of an adaptive threshold, and provides statistical assessment of the plots to determine lateralisation.

INRIAlign  Motion correction with reduced paradigmcorrelation bias
http://wwwsop.inria.fr/epidaure/Collaborations/IRMf/INRIAlign.html
alexis.roche@cea.fr (Alexis Roche)
Toolbox for spm99
A realignment routine that aims at correcting motion in fMRI sequences without generating a paradigmcorrelated bias, which is a known shortcoming of the standard 'Realignment' function.

IBZMtool  Expert system for evaluation of IBZM SPECT studies
ftp://ftp.uke.unihamburg.de/pub/nuklearmedizin/
florian.wilke@gmx.net (Florian Wilke)
Toolbox for spm2
A fully automated system for evaluation of IBZM SPECT studies. It includes automated procedures for realignment and summation of multiple frames (for motion correction), stereotactical normalization, scaling, VOIanalysis of striatal IBZM uptake, classification of striatal IBZMuptake, and standardized display.

ISAS  IctalInterictal SPECT Analysis by SPM
http://spect.yale.edu
hal.blumenfeld@yale.edu (Hal Blumenfeld)
Toolbox for spm2
ISAS analyzes the difference between an ictal and interictal SPECT scan for a single patient. The ictal/interictal differences are checked against a healthy normal database (provided) to assess the significance of CBF changes. Motified SPM files should reduce data entry errors during the statistical model configuration steps.

LItoolbox
http://www.medizin.unituebingen.de/kinder/en/research/neuroimaging/software/
Marko.Wilke@med.unituebingen.de (Marko Wilke)
Toolbox for spm8
Allows assessment of laterality effects in imaging data using various thresholding options. Amog other features, regionallyrestricted analyses are possible and a bootstrapping approach allows to assess data homogeneity to reduce the effect of outliers. The toolbox can now be scripted and batched, allowing for unattended analyses. The latest version requires spm8 (contact Marko for earlier versions).

LogTransform
http://audiofmri.langers.nl/files/logtransform.zip
Davey.Langers@nottingham.ac.uk (Dave Langers)
Toolbox for spm8,spm12
Toolbox providing batchprocessing capability to perform a logarithmic transformation on series of fMRI data. This is useful for converting signals from arbitrary scanner units to meaningful units of percentage signal change early during preprocessing already.

MARINA  MAsks for Region of INterest Analysis
http://www.bion.de/eng/MARINA.php
walter@bion.de (Bertram Walter)
Toolbox for spm2
Allows you to create, smooth, threshold, edit, and save masks in Analyze format. The creation of masks is aided by the anatomical parcellation of the brain published by TzourioMazoyer et al. (2002). Voxel coordinates of brain structures come from their SPM toolbox AAL (automated anatomical labeling).

MarsBar  MARSeille Boite A Region d'interet
http://marsbar.sourceforge.net/
matthew.brett@mrccbu.cam.ac.uk (Matthew Brett)
Toolbox for spm99,spm2,spm5,spm8
Region of interest (ROI) analysis, including ROI definition, combination of ROIs with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.

MASCOI  Masked Contrast Images
http://homepages.unituebingen.de/matthias.reimold/mascoi/
matthias.reimold@unituebingen.de (Matthias Reimold)
Toolbox for spm2,spm5
Explores results, provides atlas labels and creates bitmaps for publication figures. In particular gives a sidebyside comparison of traditionally thresholded tmaps and "masked contrast images". One of the benefits of masked contrast images is an improved spatial precision, particularly if smoothed / low resolution image data were analyzed (e.g. betweensubject statistics, PET, VBM).

mfBox  The modelfree toolbox
http://mfbox.sourceforge.net/
fabian.theis@mathematik.uniregensburg.de,petergruber@gmx.net (Peter Gruber, Fabian Theis, Ingo Keck)
Toolbox for spm5
For modelfree analysis of fMRI or PET data sets. Its graphical user interface enables users to easily try out various modelfree algorithms, together with additional pre and postprocessing algorithms and reliability analyses. The design of the toolbox is modular, so it can be easily extended to include your algorithm of choice.

Masking Toolbox
http://www.cs.ucl.ac.uk/staff/g.ridgway/masking
Ged.Ridgway@gmail.com (Ged Ridgway)
Toolbox for spm2,spm5,spm8
Creates an explicit mask defining which voxels are included in statistical analysis. Uses an automatic method that finds an optimal threshold for binarising an average image. Also offers a more flexible method (without GUI) for expert control over the mask.

Masks
http://www.anzsnm.org.au/cms/specialisations/software/spmtoolboxes/
leighton.barnden@nwahs.sa.gov.au (Leighton Barnden)
Toolbox for spm99,spm2
An SPM toolbox to mask, weight or prescale spatially normalised images. Weighting is useful for generic scalp stripping, and it also computes mean or maxima in mask.

MIPC  Maximum Intensity Projection with colors
http://www.lni.hc.unicamp.br/~beltramini
gcbeltramini@gmail.com (Guilherme Coco Beltramini)
Toolbox for spm8
MIPC is a simple program that creates a color image with the maximum intensity projection on a glass brain in three orthogonal planes.

MM  Multivariate Methods for fMRI
Contact email above
fkherif@fil.ion.ucl.ac.uk (Ferath Kherif)
Toolbox for spm99,spm5
Implements several multivariate methods for fMRI data analysis, including principal components analysis (PCA), projected PCA, multivariate linear model (MLM) and partial least squares (PLS). Useful for both exploratory and confirmatory analyses.

multifocal  Create multifocal fMRI designs
http://neuro.hut.fi/~vanni/data/Multifocal.zip
vanni@neuro.hut.fi (Simo Vanni)
Toolbox for spm2
Multifocal fMRI designs allows simultaneous measurement of local signals in the cortex from multiple visual field regions in parallel. This toolbox creates multifocal fMRI stimuli for Presentation(TM), accounting for the spatial and temporal design, size of the stimulus (Mscaling), contrast, and position in the display. Also contains a separate script to estimate the data with SPM2. Tested with matlab 7.3 running in Fedora Core 6 linux.

NIRSSPM
http://bisp.kaist.ac.kr/NIRSSPM.html
shtak@kaist.ac.kr (Jong Chul Ye & Sungho Tak)
Toolbox for spm5
NIRSSPM is a statistical parametric mapping toolbox for nearinfrared spectroscopy. Based on general linear model and Sun's tube formula, NIRSSPM not only provides activation maps of oxy, deoxy, and total hemoglobin, but also allows for the superresolution activation localization.

NS  NonStationary Cluster Extent Correction
http://fmri.wfubmc.edu/cms/software#NS
shayasak@wakehealth.edu (Satoru Hayasaka)
Toolbox for spm2,spm5
This toolbox implements the random field theory (RFT) version of cluster size inference under nonstationarity. Nonstationarity is particularly problematic in VBM (voxelbased morphometry) data, and a use of cluster pvalues has been discouraged in analyses of such data. Uses code from Keith Worsley's FMRISTAT software. Also provides cluster pvalues for F images (with or with out an assumption of stationarity).

Ortho  Visualisation and ROI analysis
http://www.eecs.umich.edu/~hernan/Public/Programs/
hernan@umich.edu (Luis Hernandez)
Toolbox for spm5,spm8
An interactive tool for visualization and ROI analysis of FMRI time series data. This tool also includes Granger Causality Analysis (use at your own risk)

TAPAS PhysIO Toolbox
http://www.translationalneuromodeling.org/documentation/
kasper@biomed.ee.ethz.ch (Lars Kasper)
Toolbox for spm8,spm12
This toolbox provides modelbased physiological noise correction of fMRI data using peripheral measures of respiration and cardiac pulsation. It incorporates noise models of cardiac/respiratory phase (RETROICOR, Glover et al. 2000), as well as heart rate variability and respiratory volume per time (cardiac response function, Chang et. al, 2009, respiratory response function, Birn et al. 2006). The toolbox is usable via the SPM batch editor, performs automatic preprocessing of noisy peripheral data and outputs nuisance regressor files directly suitable for SPM ("multiple_regressors.txt").

PSPM  Parallel SPM
http://prdownloads.sourceforge.net/parallelspm/
koola@musc.edu (Jejo Koola)
Toolbox for spm2
Parallelized SPM2. Uses MPI to parallelize coregistration and reslicing

REST  Restingstate fMRI data analysis toolkit
http://restingfmri.sourceforge.net/
dawnwei.song@gmail.com,ycg.yan@gmail.com (XiaoWei Song & ChaoGan Yan)
Toolbox for spm99,spm2,spm5,spm8
REST is an independent toolkit designed for resting state fMRI data analysis. It eases the analysis process with a GUI and contains three methods: functional connectivity, Amplitude of Low Frequency Fluctuation (ALFF) and Regional Homogeneity (ReHo).

rfxplot  Visualisation of Group Inference Data
http://rfxplot.sourceforge.net/
glascher@hss.caltech.edu (Jan Glascher)
Toolbox for spm5
rfxplot is a versatile toolbox for SPM5 which offers plotting effect sizes, fitted responses, and BOLD time courses averaged across subjects from within 2nd level (random effects) analyses. The toolbox offers a large variety of plot configuration both suitable for data exploration and producing high quality figures for publications.

RobustWLS  Robust regression using Weightedleastsquares
http://www.icn.ucl.ac.uk/motorcontrol/imaging/robustWLS.html
j.diedrichsen@ucl.ac.uk,reza@bme.jhu.edu (Joern Diedrichsen & Reza Shadmehr)
Toolbox for spm2,spm5,spm8
This toolbox implements an approach to detect and correct for artifacts in fMRI time series data, described in detail in Diedrichsen & Shadmehr (2005, Neuroimage). The robust estimate is obtained by weighting each image by the inverse of the noise variance of that image. New version has improved plotting and outlier detection.

SAfE  Straightforward Analysis of fMRI and EEGfMRI
http://www.lni.hc.unicamp.br/~beltramini
gcbeltramini@gmail.com (Guilherme Coco Beltramini)
Toolbox for spm8
Brief summary: Straightforward analysis of fMRI experiments, from the preprocessing until the statistical maps, with little user input. Especially suited for situations when the number of conditions and timing of the events vary among subjects, such as in EEGfMRI analysis. When the onset and duration of the events are obtained from the EEG, a VBA macro in Microsoft Excel reads the EEG markers file and creates the appropriate spreadsheet. GUI and batch processing.

SCRalyze
http://scralyze.sourceforge.net/
d.bach@fil.ion.ucl.ac.uk (Dominik R. Bach)
Toolbox for spm8
Modelbased analysis for peripheral psychophysiological signals (e.g. skin conductance) including GLM and DCM.

SDM  Signed Differential Mapping
http://www.sdmproject.com/
joaquim.radua@iop.kcl.ac.uk (Joaquim Radua)
Toolbox for spm5,spm8
Signed Differential Mapping is a statistical technique for metaanalyzing studies on differences in brain activity or structure which used neuroimaging techniques such as fMRI, VBM or PET. SDM adopted and combined various positive features from previous methods and introduced a series of improvements and novel features.

SimpleROIBuilder  Easy creation of simple ROIs
http://wwwpersonal.umich.edu/~rcwelsh/SimpleROIBuilder/
rcwelsh@med.umich.edu (Robert Welsh)
Toolbox for spm2,spm5
Creates mask images based on spheres or boxes.

SnPM  Statistical Nonparametric Mapping
http://warwick.ac.uk/snpm
t.e.nichols@warwick.ac.uk (Andrew Holmes & Thomas Nichols)
Toolbox for spm99,spm2,spm5,spm8,spm12
Nonparametric permutation test for PET and second level fMRI data. Gives (familywise error rate) corrected pvalues that do not depend on random field theory.

spm_wavelet  Spatial wavelet denoising
http://fs2.psychiatry.cam.ac.uk/~amw71/publications/TMI2004/TMI2004_software.html
a.m.wink@gmail.com (Alle Meije Wink)
Toolbox for spm2,spm5
Adds wavelet denoising option to smooth button. Requires additional (free) Matlab tools: WaveLab, fractional spline wavelet package, and (if SPM99 is used) the SPM99 FDR modification.

SPMd  Statistical Parametric Mapping Diagnosis
http://wwwpersonal.umich.edu/~nichols/SPMd/
spmdauthors@umich.edu (WenLin Luo & Thomas Nichols)
Toolbox for spm99,spm2,spm5
Allows you to establish the validity of inferences in fMRI modeling through diagnosis of linear model assumptions, and to characterize fMRI signal and artifacts through exploratory data analysis.

SPMMouse  animal brain toolbox for SPM
http://www.spmmouse.org/
sjs80@wbic.cam.ac.uk (Stephen Sawiak)
Toolbox for spm5
SPMMouse extends the functionality of SPM5 to the animal brain by allowing it to open and use files of any voxel dimensions. Priors are included for the mouse brain, and an interface is provided to create glass brains from any (brainextracted) image for use with the SPM results interface.

SSM PCA  A multivariate toolbox for brain mapping analysis
http://feinsteinneuroscience.org/imagingsoftware
yma@nshs.edu,pspetsie@nshs.edu (Yilong Ma and Phoebe Spetsieris)
Toolbox for spm99,spm2,spm5
This toolbox implements the multivariate Scaled Subprofile Modeling (SSM) method based on Principal Component Analysis (PCA). It can generate spatial covariance patterns from functional or anatomical brain images that can discriminate a particular disease or predict behavioral correlation in patients and controls. The toolbox is downloadable from 'software' button on the following website.

SUIT  Spatially unbiased infra tentorial template for normalization of cerebellum and brainstem
http://www.icn.ucl.ac.uk/motorcontrol/imaging/suit.htm
j.diedrichsen@ucl.ac.uk (Joern Diedrichsen)
Toolbox for spm2,spm5,spm8
Improves the intersubject normalization of infratentorial structures (cerebellum and brainstem). Contains a new highresolution and spatially unbiased atlas template plus an algorithm to seperate cerebellum and brainstem from surrounding tissue.

SurfRend  Surface rendering of statistic maps
http://spmsurfrend.sourceforge.net/
kahn@nmr.mgh.harvard.edu (Itamar Kahn)
Toolbox for spm99,spm2,spm5
Suite of scripts that create surfacebased renderings of SPM statistic maps

TemplateOMatic toolbox
https://irc.cchmc.org/software/tom.php
christian.gaser@unijena.de (Christian Gaser, Marko Wilke, Mekibib Altaye, Scott Holland)
Toolbox for spm5,spm8
Using the general linear model, it allows to statistically isolate the influence of external variables of interest on brain structure. It comes with data allowing to create pediatric templates and tissue maps based on the objective 1 NIH data (n = 404), in the age range of 518 years. It writes SPM2compatible data and now includes an option to generate customized priors for "new segment".

UF2C  User Friendly Functional Connectivity
http://www.lni.hc.unicamp.br/app/uf2c/
brunno@fcm.unicamp.br (Brunno M. Campos)
Toolbox for spm8
UF2C aims to simplify and organize functional connectivity studies in neuroimaging through a clean and validated methodology, without sacrificing quality. UF2C has a full processing pipeline: The user only needs to select the raw functional and structural NIfTI files from the subjects. The graphical user interface makes the processing and analysis options accessible for neuroscientists, with reasonable choices of default settings. UF2C allows the user to study functional connectivity both through a quantitative view that provides detailed values of average connectivity, and through a spatial view that provides statistical maps that can be directly used for further analyses. All results are carefully organized in distinct folders for each subject, and a common folder is generated with a log file reporting the quantitative results of all the analyzed subjects.

Unwarp Toolbox
http://www.fil.ion.ucl.ac.uk/spm/toolbox/unwarp/
jesper@fmrib.ox.ac.uk,chutton@fil.ion.ucl.ac.uk (Jesper Andersson & Chloe Hutton)
Toolbox for spm2
Toolbox for estimation and removal of movementbysusceptibility induced variance in fMRI time series. Allows inclusion of a measured field map which can be processed by the FieldMap Toolbox. Please note that for SPM5 and above, the Unwarp is part of the SPM distribution.

Volumes Toolbox
http://sourceforge.net/projects/spmtools
volkmar.glauche@uniklinikfreiburg.de (Volkmar Glauche)
Toolbox for spm2,spm5,spm8
This toolbox contains various functions that deal with image volumes. Utilities include tools for splitting and combining volumes (for when multiple measurements are recorded per slice), extracting time series and creating and applying mask.

Waveletbased Morphometry
http://www.wbmorphometry.com/
ejcanalesr@gmail.com (Erick J. CanalesRodriguez)
Toolbox for spm2,spm5,spm8
Waveletbased morphometry (WBM) is an alternative strategy to voxelbased morphometry (VBM) consisting in conducting the statistical analysis (i.e., univariate tests) in the wavelet domain. Note that the toolbox will work in any SPM version, but it requiresLinux / Unix or Mac OS.

Waveletbased SPM
http://miplab.epfl.ch/wspm/
Dimitri.VanDeVille@epfl.ch (Dimitri Van De Ville)
Toolbox for spm2,spm5,spm8
A new framework for the detection of brain activity from fMRI data using the wavelet transform. The framework combines powerful wavelet processing with statistical testing in the spatial domain.

WFU_PickAtlas
http://www.nitrc.org/projects/wfu_pickatlas/
maldjian@wfubmc.edu (Joseph Maldjian)
Toolbox for spm99,spm2,spm5,spm8
This software provides a method for generating ROI masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label and Tissue Type. The atlases have been extended to the vertex in MNI space (see Atlas Modifications under Technical Notes). Additional atlases can be added without much difficulty. The toolbox was developed in the Functional MRI Laboratory at the Wake Forest University School of Medicine.

xjView  Viewing tool
http://www.alivelearn.net/xjview8/
cuixiaofei@gmail.com,lijian@nyu.edu,dawnwei.song@gmail.com (Xu Cui, Jian Li, Xiaowei Song)
Toolbox for spm2,spm5,spm8
A viewing program for SPM. pvalue slider, slice viewer, displays multiple images at a time, display both positive and negative contrast at a time, anatomy description with a single mouse click, etc.

XMLTools
http://www.birncommunity.org/toolscatalog/xcedespmtoolbox/
dbkeator@uci.edu (David Keator)
Toolbox for spm2
A toolbox for SPM was created to capture the results from activation maps using the XML activation schema. The toolbox supports both SPM99 and SPM2 statistical structures and has been tested on SUN, LINUX, and Microsoft Windows operating systems. The toolbox has been used to capture PET and fMRI analysis results and the associated analysis model specifications.

AveLI
http://dx.doi.org/10.1016/j.jneumeth.2011.12.020
info.aveli@gmail.com (Kayako Matsuo)
Utility for spm5,spm8
An easytouse MATLAB script to calculate the laterality index of fMRI as described in Matsuo et al. J Neurosci Methods 2012.

BrainMagix SPM Viewer
http://www.imagilys.com/brainmagixspmviewer/
info@imagilys.com (Imagilys)
Utility for spm5,spm8
A free, professional viewer for SPM fMRI activations. JAVAprogrammed, crossplatform (Windows, MAC, Linux), without Matlab license, making it possible to share your results with colleagues who do not have SPM installed. Read SPM.mat files and NIfTI images in an userfriendly way. Overlay the blobs with an atlas or any anatomical image. On the fly adjustment of threshold and cluster size. Localize your activations in an atlas. BOLD signal curves in ROIs. Export results as PNG images.

Bruker2Analyze  Bruker Paravision to Analyze converter
http://www.mccauslandcenter.sc.edu/mricro/mricro/bru2anz/index.html
chris.rorden@mricro.com (Chris Rorden)
Utility for spm99
Windows program to convert Bruker to Analyze files.

CBMGTools  Utilities for analysis, display, etc
http://www.brain.northwestern.edu/cbmg/cbmgtools/
dgitelman@northwestern.edu (Darren Gitelman)
Utility for spm99
Tools from the Cognitive Brain Mapping Group (Northwestern University) for creating a mosaic of slices, a PSTH plot, a custom MPI. Also includes SPM modifications (aka 'hacks') for crosshairs hiding and DICOM conversion.

Design Magic  Multicollinearity assessment for fMRI designs
http://www.matthijsvink.com/tools.html
m.vink@azu.nl (Matthijs Vink)
Utility for spm99,spm2
Allows you to assess the multicollinearity in your fMRIdesign by calculating the amount of factor variance that is also accounted for by the other factors in the design (expressed in R^2). Essentially, the higher R^2 is, the lower the tvalues will be. Also can calculate (and create) the most optimal highpass filter for your design.

dicom2nifti
http://www.aimfeld.ch/neurotools/neurotools.html
neurotools@aimfeld.ch (Adrian Imfeld)
Utility for spm5,spm8
dicom2nifti converts DICOMfiles (.dcm) to NIfTIfiles (.nii or .img/.hdr). A specified directory and its subdirectories are searched for DICOMfiles. These files will then be converted to NIfTI format using SPM functions. The NIfTIfiles will be properly named, moved to a targetdirectory and sorted in subdirectories according to their type (anatomical, functional, or DTI).

Dynamic PET  Quantification of dynamic PET studies
https://www.jiscmail.ac.uk/cgibin/webadmin?A2=spm;590495cb.02
florian.wilke@rzbd.fhhamburg.de,buchert@uke.unihamburg.de (Florian Wilke & Ralph Buchert)
Utility for spm2
Fully automated modeling of dynamic PET studies using the Ichise noninvasive plot. The toolbox, inclusive example dataset, is available via email.

Easy_ROI
http://www.sbirc.ed.ac.uk/LCL/LCL_M1.html
cyril.pernet@ed.ac.uk (Cyril Pernet)
Utility for spm2,spm5,spm8
Reads and returns data of any images from a region of interest identified within the SPM result table.

Easy_Volumes
http://www.sbirc.ed.ac.uk/LCL/LCL_M1.html
cyril.pernet@ed.ac.uk (Cyril Pernet)
Utility for spm5,spm8
Returns the number of voxels and the volume of segmented modulated 3D volumes (GM, WM or CSF).

FDRill  Plot T image histogram and FDR PPplot
http://wwwpersonal.umich.edu/~nichols/FDR/FDRill.m
nichols@umich.edu (Tom Nichols)
Utility for spm2
For a given T image plots the histogram (rootogram, actually) and the loglog PP plot, which illustrates how the FDR threshold is found. Can be used interactively or scripted.

Fluctuation  Taskindependent connectivity discussion group
http://www.nitrc.org/projects/fluctuations
handwerkerd@mail.nih.gov (Daniel Handwerker)
Utility for spm99,spm2,spm5
Discussion group that focus on the methodology and applications of task independent fluctuation measures including: connectivity maps of fMRI resting state scans, research using EEG/MEG/PET etc, methods to remove nonneural fluctuations, and applications to clinical populations.

fToolbelt  Functional Toolbelt
http://web.eecs.umich.edu/~hernan/Public/Programs/Mfiles/
hernan@umich.edu (Luis Hernandez)
Utility for spm99
MATLAB functions for visualization, time series extraction, and trial averaging. C programs for slice timing correction, ASL syncsubtraction, spheres extractions. Shell scripts for image management, .... and a few other tools.

Fractional Anisotropy Database
http://rad.med.hokudai.ac.jp/research/fa/
dti@radi.med.hokudai.ac.jp (Khin Khin Tha)
Utility for spm2
A database representing normal fractional anisotropy values for the age (2069 years) and sex of individual.

GA  Genetic Algorithm for Experimental Design
http://www.columbia.edu/cu/psychology/tor/genetic_algorithms.html
tor@paradox.psych.columbia.edu (Tor Wager)
Utility for spm99,spm2,spm5,spm8
Optimizes event related fMRI designs by statistical and psychological criterion. (Matlab Signal Processing Toolbox required).

GE2SPM  Convert data from GE to SPM Analyze
http://web.archive.org/web/20030622131151/http://dbic.dartmouth.edu/~inati/tools/ge2spm.php
souheil.inati@dartmouth.edu (Souheil Inati)
Utility for spm99
Create SPM compatible Analyze images, including the .mat file to relate image coordinates to scanner coordinates.

GIFT  Group ICA of fMRI Toolbox
http://mialab.mrn.org/software/
vcalhoun@unm.edu (Vince Calhoun)
Utility for spm2,spm5
Implements multiple algorithms for ICA of group (and single subject) fMRI data.

JG  John's Gems
http://wwwpersonal.umich.edu/~nichols/JohnsGems.html
john@fil.ion.ucl.ac.uk (John Ashburner)
Utility for spm99,spm2,spm5
Essential Code Snippets by John Ashburner, extracted from the SPM email help list. Most tips are for SPM99 and SPM2, though there are some for SPM5.

L2S  LORETA to SPM
http://www.ihb.spb.ru/~pet_lab/L2S/L2SMain.htm
sergey@ihb.spb.ru (Sergey Pakhomov)
Utility for spm99
Converts output data from LORETA into SPM compatible format.

log_roi_batch  Script for ROI value extraction
http://www.aimfeld.ch/neurotools/neurotools.html
neurotools@aimfeld.ch (Adrian Imfeld)
Utility for spm5,spm8
log_roi_batch creates tables of mean or standard deviation for regions of interest (ROIs) or counts voxels with values within a given range. Voxel exclusion criteria can be specified, which can also be used to count the number of included or excluded voxels within a given value range.

LMGS  Remove global effects from fMRI images
http://code.google.com/p/lmgs4spm/
pmacey@ucla.edu (Paul Macey)
Utility for spm2,spm5,spm8
Detrend fMRI timeseries of any components matching the global signal. This method is a very conservative approach to dealing with global influences, removing at each voxel any linear component matching the global signal (LMGS = Linear Model of the Global Signal, at each voxel). Based on Macey et al., NI 2004; 22(1):3606.

Motion Fingerprint
http://www.medizin.unituebingen.de/kinder/en/research/neuroimaging/software/
Marko.Wilke@med.unituebingen.de (Marko Wilke)
Utility for spm8
Allows to generate a more comprehensive indicator of motion (combining translation and rotation) as well as a motion mask and a "motion fingerprint", characterizing the effects of motion in this individual timeseries. Interactive or scripted use

mri_toolbox  Analyze read/write utilities
http://eeg.sourceforge.net
Darren.Weber@radiology.ucsf.edu (Darren Weber)
Utility for spm99
A matlab toolbox for reading, writing and viewing Analyze slices and volumes. It provides endian conversions and simple options for orthogonal reslicing. The GUI requires at least Matlab 6.0 but I/O functions should work under matlab 5.x.

MSU  MNI Space Utility
http://www.ihb.spb.ru/~pet_lab/MSU/MSUMain.html
sergey@ihb.spb.ru (Sergey Pakhomov)
Utility for spm99,spm2,spm5
Visualization of SPM99 clusters in terms of Talairach Daemon anatomical region labels, but converting MNI coordinates of data to Talairach coordinates.

Orthviews Plugins  Reorient, Diffusion tensor visualization, and more!
http://sourceforge.net/projects/spmtools
volkmar.glauche@uniklinikfreiburg.de (Volkmar Glauche)
Utility for spm2,spm5
Plug in for SPM's spm_orthviews (accessed from "Check Reg" button). From popup menu can reorient, visualize diffusion tensors, use a movie tool to step through slices or create ROI masks.

PCT  Percent Change Threshold
http://wwwpersonal.umich.edu/~nichols/PCT/
nichols@umich.edu (Thomas Nichols)
Utility for spm99
Reexpresses standard deviation in useful units, the minimum percent change required to obtain a significant result.

pvconv.p  A Bruker data converter
http://pvconv.sourceforge.net/
matthew.brett@mrccbu.cam.ac.uk (Matthew Brett)
Utility for spm99
Converts Bruker format MRI data to Analyze or MINC image format; based on converters by Andrew Janke (MINCtools).

r2agui  A Philips PAR/REC to Analyze/NifTI data converter
http://r2agui.sourceforge.net
b.neggers@umcutrecht.nl (Bas Neggers)
Utility for spm2,spm5
Automatically batchconverts V3 (Philips Intera scanner family) and V4 (Philips Intera scanner family) data formats to Analyze 7.5 or NIfTI 1.0. Has graphical user interface. Report bugs to https://sourceforge.net/projects/r2agui/

SEM  Structural Equation Modelling (SEM) for fMRI
http://dslink333.dlinkddns.com/SEM.htm
d.steele@dundee.ac.uk (Douglas Steele)
Utility for spm99,spm2,spm5,spm8
Allows a MATLAB based Structural Equation Modelling (SEM) calculation for fMRI data. An example is used to illustrate potential pitfalls and solutions.

slice_overlay
http://imaging.mrccbu.cam.ac.uk/imaging/DisplaySlices
matthew.brett@mrccbu.cam.ac.uk (Matthew Brett)
Utility for spm2
Shows images in a series of slices in a matlab figure window. It can be used to display a single image, such as a structural scan, or a composite image, where activation has been overlaid on the structural scan.

TSDiffAna  translates somehow into timeseries difference analysis
http://sourceforge.net/projects/spmtools
volkmar.glauche@uniklinikfreiburg.de (Matthew Brett, Volkmar Glauche)
Utility for spm2,spm5,spm8
Computes slicewise scan by scan difference and standard deviations. Useful to examine quality of image timeseries. Scans or slices that show deviations from timeseries mean may be corrupt and need more detailed inspection.

TSU  Talairach Space Utility
http://www.ihb.spb.ru/~pet_lab/TSU/TSUMain.html
sergey@ihb.spb.ru (Sergey Pakhomov)
Utility for spm99,spm2,spm5
Visualization of SPM99 clusters on Talairach atlas sections.

iTT Toolbox
http://www.biomednmr.mpg.de/index.php?option=com_content&task=view&id=37&Itemid=43
tauer@gwdg.de (Tibor Auer)
Utility for spm5,spm8
This toolbox implements the iterative TwoThreshold (iTT) approach to correct height thresholds in SPM.

VBMtools  Collection of scripts and hints for VBM
http://dbm.neuro.unijena.de/vbm/
christian.gaser@unijena.de (Christian Gaser)
Utility for spm2,spm5,spm8
A collection of extensions to the segmentation algorithm of SPM2, SPM5 and SPM8 to provide voxelbased morphometry (VBM). Includes regularized segmentation and longitudinal anlayses.

vis  SPM image visualization
http://tools.robjellis.net
robjellis@gmail.com (Rob Ellis)
Utility for spm5,spm8
Utility that will (1) plot histograms of voxel values in an SPM, (2) display a surface plot of voxel values at a particular axial slice, or (3) display a scatter plot and calculate a Pearson correlation of values in corresponding voxel locations between two SPMs.

visionToSPM  SIEMENS Vision to SPM Analyze converter
http://www.charite.de/ch/neuro/forschung/teams/klinisch/people/thees/thees_frameset.htm
sebastian.thees@charite.de (Sebastian Thees)
Utility for spm99
Converts SIEMENS Vision ACRNEMA files (*.ima) to SPM Analyze, in particular preserving the orientation/position information.

VoiTool  Volume of Interest Tool
http://www.ihb.spb.ru/~pet_lab/VTO/VTOMain.html
sergey@ihb.spb.ru (Sergey Pakhomov)
Utility for spm99
Analyzes VOIs, including predifined Talairach VOIs, mask image saving and ascii data output.

aa  Automatic Analysis
https://github.com/rhodricusack/automaticanalysis/wiki
rhodri@cusacklab.org (Rhodri Cusack)
UtilityBatch utility for spm5,spm8
An easytouse scripting system. Choose a default recipe and preprocess all your data with just 7 lines of matlab. Add further lines to override the default processing parameters or modify pathway. Modular design, easy to program. Restartable  if it crashes, just rerun and it will start where it left off. Benchmarking facility. Easy to update as modules are stored centrally.

AutoSPET
http://www.autospet.altervista.org/
veltri@unicz.it (Pierangelo Veltri et al.)
UtilityBatch utility for spm5
AutoSPET (Automatic SPM tool invocation for PET analysis images), is a useful graphical user interface to improve efficiency in running SPM experiments. It handles the entire workflow, starting from the conversion of DICOM files, continuing on the part of preprocessing/statistics and ending finally with the running of the algorithm of classification of obtaining files mdata.

Batch AAL
https://github.com/ateshkoul/NeuroImaging/tree/master/spm/batch_aal
ateshkoul15@gmail.com (Atesh Koul)
UtilityBatch utility for spm8
Once in the matlab path, config file loads itself and the program can be viewed in spm8 batch interface. It can then be used to run automated analysis in batch. The batch file would be helpful in automating the labeling procedure and can be integrated in a full analysis (preprocessing, first level, results and labeling). The batch script can be evoked from spm8 batch interface. In batch interface: SPM > Tools > AAL.

KUL  KULeuven functions to automate SPM (fMRI)
http://www.kuleuven.ac.be/radiology/Research/fMRI/kulSPM/
stefan.sunaert@uz.kuleuven.ac.be,Erik.Beatse@uz.kuleuven.ac.be (Stefan Sunaert & Erik Beatse)
UtilityBatch utility for spm99
Automate fMRI data post processing.

parallelize_matlabbatch
http://algoholic.eu/parallelize_matlabbatch/
s.adaszewski@gmail.com (Stanislaw Adaszewski)
UtilityBatch utility for spm8
This script loads selected SPM batch, tries to intelligently guess which fields are potential candidates for "parallel splits" and after interactively asking for confirmation splits your batch into multiple .mat, .m and .sh files (placing them in the same directory as the original batch)  the latter being ready for submission to Sun Grid Engine queue. Splits are done 1:1, meaning that all the fields you select must have the same size. Tested with: NewSegment, Run DARTEL (existing Templates) and Normalize to MNI Space.

spm_segment
http://www.nmrgroup.ion.ucl.ac.uk/atrophy/index.html
j.jackson@ion.ucl.ac.uk (Jon Jackson)
UtilityBatch utility for spm99,spm2,spm5
A GUI and command line interface to measure GM/WM/CSF volumes from a series of 3D volume images. Option to separately measure lesion volume (eg Multiple Sclerosis lesions). Uses thresholding of the SPM probability maps to generate binary GM/WM/CSF masks, from which volumes are calculated.

spm2batch
http://spm2batch.sourceforge.net/
S.F.W.Neggers@fss.uu.nl (Bas Neggers)
UtilityBatch utility for spm2
Batch engine for SPM2. Includes basic preprocessing, model estimation, contrast setup, group stats. Runs multiple session designs. Tested on Linux and Windows XP, matlab 6.5. An example analysis setup script is provided.

spm2batch
http://prdownloads.sourceforge.net/spm2batch/
koola@musc.edu (Jejo Koola)
UtilityBatch utility for spm2
A batch system SPM2, including commandline specification of slice_timing options. Tested on Matlab 6.1 & 6.5.

spm2Batch
http://wwwpersonal.umich.edu/~rcwelsh/spm2Batch/
rcwelsh@med.umich.edu (Robert Welsh)
UtilityBatch utility for spm2
Batch scripts that run from the Unix command line. Matlab scripts are created and run in the background and will send an email when complete.

spmbatch
http://www.aimfeld.ch/neurotools/neurotools.html
neurotools@aimfeld.ch (Adrian Imfeld)
UtilityBatch utility for spm5,spm8
spmbatch (former spm5batch) creates and runs SPMjobs for multiple subjects by replacing paths in a given templatejob. Jobs on the first level (single subject) are supported, e.g. preprocessing of fMRI data, firstlevel statistics, image calculator, check registration, jobs with external SPM toolboxes.

spmjob
http://sourceforge.net/projects/spmjob/
tanner@gmx.de (Thomas Tanner)
UtilityBatch utility for spm2
A wrapper for the SPM2 batch interface which provides a GUI for setting all parameters. Supports preprocessing, parameter estimation, contrasts and second level analysis. spmjob has both flexible scripting support and a user friendly GUI.

X_batch
http://xbatch.sourceforge.net
biostr@users.sourceforge.net (Xenia Hertzenberg)
UtilityBatch utility for spm2
Integrates Protege ontology and SPM2 batch processing utility. It does both the preprocessing and stats, though not the results.

Zephyr
http://prefrontal.org/wiki/index.php/Zephyr
craig.bennett@dartmouth.edu (Craig Bennett)
UtilityBatch utility for spm2
Batch processing system for SPM2. Note, contains rawdata conversion function which will need to be modified for other sites.

B2K template images for neuroimaging in baboon
http://purl.org/net/kbmd/b2k
kevin@wustl.edu (Kevin Black)
Templates for spm99
T1weighted MRI template based on 9 normal baboons, and PET template based on [15O]water PET images of 7 baboons.

Brain Atlases of 2yearolds
http://www.braindevelopment.org/
D.Rueckert@imperial.ac.uk (Daniel Rueckert)
Templates for
33 brain atlases of two year old subjects, of 83 regions each, together with their related MRIs

Probabilistic atlas of the human cerebellum
http://www.icn.ucl.ac.uk/motorcontrol/imaging/propatlas.htm
j.diedrichsen@bangor.ac.uk (Joern Diedrichsen)
Templates for
A probabilistic atlas of the cerebellar lobules in the anatomical space defined by the MNI152 template, obtained from T1weighted MRI scans (1mm isotropic resolution) of 20 healthy young participants.

CCHMC Pediatric Atlas
http://www.irc.cchmc.org/software/pedbrain.php
Marko.Wilke@med.unituebingen.de (Marko Wilke)
Templates for spm99,spm2
GM and WM template defined with 200 children aged 5 to 18. Created for SPM99 but SPM2 compatible (for SPM5, use the TemplateOMatic toolbox listed above).

DementiaSpecific [18F]FDGPET template for SPM normalization
http://inlab.ibfm.cnr.it/PET_template.php
pasquale.dellarosa@ibfm.cnr.it,perani.daniela@hsr.it (Pasquale Anthony Della Rosa & Daniela Perani)
Templates for spm99,spm2,spm5,spm8,spm12
The DementiaSpecific [18F]FDGPET template (after spatial normalization of [18F]FDGPET images) from 100 images (50 controls and 50 patients). The EADC PET group has contributed 113 cases for the healthy normal dataset, and 48 for the template. The EADC PET group is made of scientists at Hosp S Martino, Genova (IT); IRCCS Fatebenefratelli and Hosp Civile, Brescia (IT); Vrije Universiteit Medical Centre, Amsterdam (NL); Technische Universitet Munich, Munich (GE); and Hopitaux de Marseille, Marseille (FR).

Template images for neuroimaging in Macaca fascicularis
http://purl.org/net/kbmd/cyno
kevin@wustl.edu (Kevin Black)
Templates for spm99
T1weighted MRI template based on 11 normal cynomolgus monkeys.

MRI template of Macaca Fascicularis Brain
http://www.cima.es/labsen/instrumentaltechniquesmicropet/technologies/1
eprietoaz@unav.es (Maria Collantes & Elena Prieto )
Templates for
T1weighted MRI, 18FDOPA PET and 11CDTBZ PET templates based on 15 healthy Macaca Fascicularis subjects, available in Analyze format.

112RMSL template images for neuroimaging in rhesus macaque (Macaca mulatta)
http://brainmap.wisc.edu/monkey.html
dm10@medicine.wisc.edu (Donald McLaren)
Templates for spm5,spm8
T1weighted MRI template based on 112 adult Macaca mulattas (30 females), tissue priors, and T2weighted MRI template (9 monkeys) aligned to Saleem and Logothetis Atlas (2006). Transformation parameters to F99 space are also available. Additionally, a technical report is included. A paper by McLaren et al. is in press at NeuroImage.

N2K template images for neuroimaging in Macaca nemestrina
http://purl.org/net/kbmd/n2k
kevin@wustl.edu (Kevin Black)
Templates for spm99
T1weighted MRI template based on 11 normal nemestrinas, and PET template based on [15O]water PET images from 9 of the 11.

Karolinska Rat Atlas
http://expmr.ki.se/research/ratatlas.jsp
christian.spenger@ki.se (Christian Spengere)
Templates for spm99
"Paxinos space" rat template based on five adult female SpragueDawley rats.

18FDOPA and 123IFPCIT human templates for SPM normalisation
http://www.nitrc.org/projects/spmtemplates
javier191185@gmail.com (GarciaGomez F.J., GarciaSolis D.)
Templates for spm5,spm8
18FDOPA PET template (after spatial normalization of T1weighted MRI images) from 10 healthy humans, and 123IFPCIT SPECT template from 26 healthy humans.

UNC 012 Infant Atlases
http://www.nitrc.org/projects/pediatricatlas
fengshi@med.unc.edu (Feng Shi)
Templates for
There are 3 atlases dedicated for neonates (T2), 1yearolds (T1), and 2yearolds (T1). Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map.

Zebra Finch MRI Atlas
https://www.uantwerpen.be/en/rg/bioimaginglab/research/mriatlases/zebrafinchbrainatlas/
colline.poirier@ua.ac.be (Colline Poirier)
Templates for spm99,spm2
Threedimensional MRI atlas of the zebra finch brain, available in Analyze format.