SPM Extensions
http://www.fil.ion.ucl.ac.uk/software/spm/ext/
Statistical Parametric Mapping Extensionsnichols@umich.edu (Tom Nichols)http://blogs.law.harvard.edu/tech/rss1440AAL - Anatomical Automatic Labeling
http://www.gin.cnrs.fr/AAL
aal.gin.brainatlas@gmail.com (Gin)Toolbox for spm99,spm2,spm5,spm8,spm12Automated parcellation method, as described in Tzourio-Mazoyer et al. NI 2002.AAL2 - Anatomical Automatic Labeling2
http://www.gin.cnrs.fr/AAL2
aal.gin.brainatlas@gmail.com (Gin)Toolbox for spm12Implementation of a new parcellation of the orbitofrontal cortex in the automated anatomical labeling atlas, as described in Rolls et al. NI 2015.ACID - Artefact correction in diffusion MRI
http://www.diffusiontools.com/
siawoosh.mohammadi@ucl.ac.uk (Siawoosh Mohammadi)Toolbox for spm8,spm12The Artefact correction in diffusion MRI (ACID) toolbox is an academic software toolkit for pre-processing of diffusion MRI data, estimation of DTI indices and normalisation of DTI index maps, which fully integrates into the batch system of SPM8.AICHA - An atlas of intrinsic connectivity of homotopic areas
http://www.gin.cnrs.fr/AICHA
aicha.gin.brainatlas@gmail.com (Gin)Toolbox for spm12An atlas of intrinsic connectivity of homotopic areas, as described in Joliot et al. J Neuroscience Methods 2015.ALI - Automated Lesion Identification
Contact email above
mseghier@gmail.com (Mohamed Seghier)Toolbox for spm5,spm8,spm12ALI is a research tool for lesion delineation and spatial normalization for patients with brain damage. It uses the unified normalisation-segmentation algorithm with an explicit extra prior for the lesion that is refined iteratively in a patient-specific manner. Lesions are then defined as a set of outlier voxels while taking into account the typical variability in anatomy in healthy controls. ALI can also generate lesion overlap maps.ALVIN - Automatic Lateral Ventricle delIneatioN
http://sites.google.com/site/mrilateralventricle/
matthew.kempton@kcl.ac.uk (Matthew Kempton)Toolbox for spm8Segmentation of the lateral ventricles validated in infants, adults and patients with Alzheimer's disease. Works with both T1 and T2 images.AMAT: A meta-analysis toolbox
http://www.antoniahamilton.com/amat.html
antonia.hamilton@nottingham.ac.uk (Antonia Hamilton)Toolbox for spm2AMAT 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/ni-stat/AnalyzeMovie.tar
rcwelsh@med.umich.edu (Robert Welsh)Toolbox for spm99Create AVI movies from Analyze images, of axial, coronal, sagittal or ortho slices. Requires Matlab6 or greater.Anatomy - SPM Anatomy toolbox
http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html
S.Eickhoff@fz-juelich.de (Simon Eickhoff)Toolbox for spm99,spm2,spm5,spm8This toolbox integrates probabilistic cytoarchitectonic maps derived from human post-mortem studies into the SPM environment and provides a wide range of different approaches to analyse structure / function correlations.AQuA
http://www.ibime.upv.es/mi/
lnjuanj@gmail.com (Antonios Antoniou and Juan J. Lull)Toolbox for spm5AQuA 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.ArtRepair - Artifact Repair toolbox
http://cibsr.stanford.edu/tools/human-brain-project/artrepair-software.html
mazaika@stanford.edu (Paul Mazaika)Toolbox for spm2,spm5,spm8,spm12Special 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.aslm - a slightly modified asl-module
http://aslm.sourceforge.net
homan@puk.unibe.ch (Philipp Homan)Toolbox for spm8aslm 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,spm12ASLtbx 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 SPM5-based 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/at-4-fmri/
cyril.pernet@ed.ac.uk (Chris Filo Gorgolewski and Cyril Pernet)Toolbox for spm8Allow to obtain a threshold for cluster FDR - the method fits a Gamma-Gaussian mixture model to the SPM-T and finds the optimal threshold (crossing between noise and activation). Optionally write the thresholded maps.aws4SPM
http://www.wias-berlin.de/software/aws4SPM/
tabelow@wias-berlin.de (Devy Hoffmann and Karsten Tabelow)Toolbox for spm2,spm5,spm8Structural adaptive smoothing fMRI data as described in Tabelow et al. NI (2006).BFAST3D - Bayesian Fast Accurate Spatial Tricks in 3D
https://github.com/psiden/BFAST3D
per.siden@liu.se (Per Siden)Toolbox for spm12Extends SPM's Bayesian single-subject fMRI analysis to allow for estimation by MCMC and the Spatial VB method as described in Siden et al. (2016).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 connectivity-based 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 multi-modal MRI data during the last 3 years.BredeQuery
http://neuro.imm.dtu.dk/wiki/BredeQuery
bw@imm.dtu.dk (Bartlomiej Wilkowski)Toolbox for spm5BredeQuery plugin for SPM5 - enables coordinate-based meta-analytic search of related literature for brain regions directly from SPM5 environment. The coordinate-based search is performed using Finn Aarup Nielsen's Brede Database. Works with coordinates in Talairach and MNI space, MNI-to-Talairach 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).Bruker2nifti
https://github.com/CristinaChavarrias/Bruker2nifti
cristina.chavarrias@gmail.com (Cristina Chavarrias)Toolbox for spm5,spm8,spm12Bruker raw (Paravision 6) to Nifti converter.bspmview
http://spunt.github.io/bspmview/
bobspunt@gmail.com (Bob Spunt)Toolbox for spm8,spm12Another SPM viewing program. Intuitive and customizable user interface for exploring statistical images (e.g., spmT*), including display of positive and/or negative effects; voxel- and cluster-level thresholding; instant anatomical labeling; and customizable color maps. Easily generate customizable surface renderings. Save thresholded whole-brain maps, specific clusters, and ROIs. View results tables interactively, and save publication-ready tables. Although built for viewing statistical images, it allows viewing other image types (e.g., contrast/mask/ROI images).Computational Anatomy Toolbox
http://www.neuro.uni-jena.de/cat/
christian.gaser@uni-jena.de,robert.dahnke@uni-jena.de (Christian Gaser and Robert Dahnke)Toolbox for spm12This toolbox provides diverse morphometric methods for computational anatomy such as voxel-based morphometry (VBM), surface-based morphometry (SBM), deformation-based morphometry (DBM), and region- or label-based morphometry.CCA-fMRI
http://cca-fmri.sourceforge.net/
magnus@imt.liu.se (Magnus Borga)Toolbox for spm2,spm5The CCA-fMRI utilizes canonical correlation analysis in combination with the Balloon model and adaptive filtering of fMRI data to detect areas of brain activation. The CCA-fMRI 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 spm8Multivariate kernel-based pattern classification using support vector machines (SVM) with a novel modification to obtain more balanced sensitivity and specificity on unbalanced data-sets (i.e. those with very different numbers of cases in each group).Clinical Toolbox
http://www.mccauslandcenter.sc.edu/CRNL/clinical-toolbox
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 segmentation-normalization (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://loft-lab.org/index-5.html
jiongwang@mednet.ucla.edu (Anitha Priya Krishnan, Jun Fang, Robert Smith, Danny JJ Wang )Toolbox for spm8Complexity is a toolkit used to analyze the complexity of resting state fMRI (rs-fMRI) data. Pre-processing 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 Toolbox
https://www.nitrc.org/projects/conn
alfnie@gmail.com (Alfonso Nieto-Castanon)Toolbox for spm8,spm12Performs functional connectivity analyses of fMRI data. Methods: Rest- and task- related connectivity. CompCor method for removing physiological and other confounds. First-level univariate and multivariate regression and bivariate and semipartial correlation connectivity measures. Seed-to-voxel and ROI-to-ROI 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 spm8Easy 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 singular-value 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://github.com/SPM/DAiSS
v.litvak@ucl.ac.uk (Vladimir Litvak)Toolbox for spm12SPM12 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 spm5This 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 - Post-processing for diffusion weighted image series
http://sourceforge.net/projects/spmtools
volkmar.glauche@uniklinik-freiburg.de (Volkmar Glauche)Toolbox for spm2,spm5,spm8,spm12Post-processing 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.DPABI - Data Processing & Analysis of Brain Imaging
http://dpabi.org/
ycg.yan@gmail.com (Chao-Gan Yan)Toolbox for spm8A toolbox for Data Processing & Analysis of Brain Imaging, evolved from DPARSF.DPARSF- Data Processing Assistant for Resting-State fMRI
http://rfmri.org/DPARSF
ycg.yan@gmail.com (Chao-Gan Yan)Toolbox for spm5,spm8DPARSF is a convenient plug-in 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 small-world 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 spm8The 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 respiration-induced 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 spm2Fully automated model-based 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://www-personal.umich.edu/~rcwelsh/ExtractVals.tar
rcwelsh@med.umich.edu (Robert Welsh)Toolbox for spm2Given a ROI binary mask image, this toolbox will extract values and report mean and variance.F-ASL - Arterial Spin Labeling functional MRI data
http://web.eecs.umich.edu/~hernan/Public/Programs/
hernan@umich.edu (Luis Hernandez)Toolbox for spm5,spm8An 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,spm12FAST is an EEG toolbox that can clean your EEG signal from the artefacts generated by the simultaneous acquisition of EEG-fMRI 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,spm12This 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 voxel-to-voxel 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://www-personal.umich.edu/~nichols/FDR/
nichols@umich.edu (Thomas Nichols)Toolbox for spm99Adds FDR-corrected p-values and thresholds to SPM99 results pageFieldMap Toolbox
http://www.fil.ion.ucl.ac.uk/spm/toolbox/fieldmap/
chutton@fil.ion.ucl.ac.uk (Jesper Andersson & Chloe Hutton)Toolbox for spm2Toolbox 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.mrc-cbu.cam.ac.uk/imaging/FmReference
rhodri.cusack@mrc-cbu.cam.ac.uk (Rhodri Cusack)Toolbox for spm99Uses a measured field map to undistort EPI images.FieldTrip
http://fieldtrip.fcdonders.nl/
r.oostenveld@fcdonders.ru.nl (Robert Oostenveld)Toolbox for spm8,spm12FieldTrip is a MATLAB toolbox for MEG and EEG analysis. It includes algorithms for simple and advanced analysis of MEG and EEG data, such as time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing.fMRIPower
http://fmripower.org/
jeanette.mumford@gmail.com (Jeanette Mumford )Toolbox for spm5,spm8This tool is based on the work outlined in Mumford & Nichols, NeuroImage, 39(1):261-8, 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 spm5fOSA is a software package for the processing and analysis of functional neuroimaging data using Near Infrared Spectroscopy (NIRS).gPPI
http://www.nitrc.org/projects/gppi
mclaren.donald@gmail.com (Donald McLaren)Toolbox for spm8An automated toolbox for a generalized form of psychophysiological interactions for SPM and FSFAST. The generalized form of context-dependent PPI approach ('cond' option) has increased flexibility of statistical modeling, and potentially improves model fit, specificity to true negative findings, and sensitivity to true positive findings. When using the toolbox, please cite "A Generalized Form of Context-Dependent Psychophysiological Interactions (gPPI): A Comparison to Standard Approaches", McLaren et al. NeuroImage 2012.GraphVar - comprehensive graph analyses of functional brain connectivity
http://www.rfmri.org/GraphVar
Johann.Kruschwitz@charite.de (Johann Kruschwitz)Toolbox for GraphVar is a user-friendly GUI-based toolbox for comprehensive graph-theoretical analyses of brain connectivity, including network construction and characterization, statistical analysis on network topological measures, network based statistics, and interactive exploration of results.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,spm8This 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.jung-diagnostics.de/eng/tools.php
service@jung-diagnostics.de (jung diagnostics GmbH)Toolbox for spm8HV is a SPM toolbox fully integrated into the SPM 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 Aleman-Gomez)Toolbox for spm2,spm5A 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,spm8The iBrain analysis toolbox for SPM is a free toolbox that provides an automated processing pipeline for various single- or multi-subject and/or multi-session functional neuroimaging experiments. The pipeline includes image conversion from scanner-specific formats, pre-processing, statistical analysis, region-of-interest 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 block-design, event-related, 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,spm8The iBrain Laterality Toolbox contains MATLAB scripts that implement an objective threshold-independent 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 paradigm-correlation bias
http://www-sop.inria.fr/epidaure/Collaborations/IRMf/INRIAlign.html
alexis.roche@cea.fr (Alexis Roche)Toolbox for spm99A realignment routine that aims at correcting motion in fMRI sequences without generating a paradigm-correlated bias, which is a known shortcoming of the standard 'Realignment' function.IBZM-tool - Expert system for evaluation of IBZM SPECT studies
ftp://ftp.uke.uni-hamburg.de/pub/nuklearmedizin/
florian.wilke@gmx.net (Florian Wilke)Toolbox for spm2A 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, VOI-analysis of striatal IBZM uptake, classification of striatal IBZM-uptake, and standardized display.ISAS - Ictal-Interictal SPECT Analysis by SPM
http://spect.yale.edu
hal.blumenfeld@yale.edu (Hal Blumenfeld)Toolbox for spm2ISAS analyzes the difference between an ictal and interictal SPECT scan for a single patient. The ictal/inter-ictal 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.lead-dbs
http://www.lead-dbs.org/
Andreas.Horn@charite.de (Andreas Horn)Toolbox for spm8,spm12A MATLAB Toolbox for DBS electrode reconstructions and visualizations based on postoperative MRI and CT imaging.lesion_gnb Toolbox
https://www.researchgate.net/profile/Joseph_Griffis/contributions
joegriff@uab.edu (Joseph Griffis)Toolbox for spm12The toolbox is designed for automatically classifying voxels that correspond to chronic stroke lesions in T1-weighted MRI scans. It utilizes the SPM12 New Segment and Normalization routines to obtain template-normalized patient tissue probabilistic maps (TPMs) from T1-weighted scans. These TPMs are used along with the prior probability maps (PPMs) to construct feature maps encoding information about which voxels are likely to correspond to missing and abnormal tissue. The feature maps are input as predictors to a fully trained and cross-validated Gaussian Naive Bayes classifier to obtain predictions about which voxels correspond to lesioned tissue. Simple post-processing (smoothing and cluster thresholding) can be applied to reduce the occurrence of false positives. No control group is necessary for lesion. The toolbox includes the option for obtaining and post-processing individual patient lesion predictions entirely via a simple dialogue-based interface, and also includes examples scripts for running batch jobs.LI-toolbox
http://www.medizin.uni-tuebingen.de/kinder/en/research/neuroimaging/software/
Marko.Wilke@med.uni-tuebingen.de (Marko Wilke)Toolbox for spm8,spm12Allows assessment of laterality effects in imaging data using various thresholding options. Among other features, regionally-restricted 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.LogTransform
http://audio-fmri.langers.nl/files/logtransform.zip
Davey.Langers@nottingham.ac.uk (Dave Langers)Toolbox for spm8,spm12Toolbox providing batch-processing 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.Mantis
http://developmentalimagingmcri.github.io/mantis/
richard.beare@mcri.edu.au (Richard Beare)Toolbox for spm12The morphologically adaptive neonate tissue segmentation toolbox. Two phase tissue classification for T2 weighted scans of neonates. It uses morphological segmentation and filtering to deal with hyper intense white matter and enlarged ventricles, common in scans of premature neonates.MARINA - MAsks for Region of INterest Analysis
http://www.bion.de/eng/MARINA.php
walter@bion.de (Bertram Walter)Toolbox for spm2Allows 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 Tzourio-Mazoyer et al. (2002). Voxel coordinates of brain structures come from their SPM toolbox AAL (automated anatomical labeling).MARS - Morphologically and Anatomically accuRate Segmentation
http://neuralengr.com/mars/
andypotatohy@gmail.com,yhuang16@citymail.cuny.edu (Yu (Andy) Huang)Toolbox for spm8MARS is an extended toolbox for SPM software. It is developed based on the SPM8 toolbox "New Segment". MARS added the morphological constraints on neighboring tissue voxels encoded by Markov Random Field (MRF). This MRF information is added into the updating equation of the E-step of the algorithm, not just as a post-processing step. Compared to the New Segment, the resulting segmentation is shown to be more smooth and with less discontinuities, while at the same time the accuracy is not significantly changed.MarsBar - MARSeille Boite A Region d'interet
http://marsbar.sourceforge.net/
matthew.brett@mrc-cbu.cam.ac.uk (Matthew Brett)Toolbox for spm99,spm2,spm5,spm8,spm12Region 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.uni-tuebingen.de/matthias.reimold/mascoi/
matthias.reimold@uni-tuebingen.de (Matthias Reimold)Toolbox for spm2,spm5Explores results, provides atlas labels and creates bitmaps for publication figures. In particular gives a side-by-side comparison of traditionally thresholded t-maps 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. between-subject statistics, PET, VBM).mfBox - The model-free toolbox
http://mfbox.sourceforge.net/
fabian.theis@mathematik.uni-regensburg.de,petergruber@gmx.net (Peter Gruber, Fabian Theis, Ingo Keck)Toolbox for spm5For model-free analysis of fMRI or PET data sets. Its graphical user interface enables users to easily try out various model-free 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,spm8Creates 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/spm-toolboxes/
leighton.barnden@nwahs.sa.gov.au (Leighton Barnden)Toolbox for spm99,spm2An SPM toolbox to mask, weight or pre-scale spatially normalised images. Weighting is useful for generic scalp stripping, and it also computes mean or maxima in mask.MIP-C - Maximum Intensity Projection with colors
http://www.lni.hc.unicamp.br/~beltramini
gcbeltramini@gmail.com (Guilherme Coco Beltramini)Toolbox for spm8MIP-C 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,spm5Implements 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 spm2Multifocal 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 (M-scaling), 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.MR Tool - Intensity Inhomogeneity Correction
http://www.bindgroup.eu/wp-content/uploads/2015/11/mrtool-v1.2.zip
dante.mantini@faber.kuleuven.be (Marco Ganzetti)Toolbox for spm12Intensity Inhomogeneity Correction of Structural MR Images: A Data-Driven Approach to Define Input Algorithm Parameters in SPM.MR Tool - Multimodal Mapping
http://www.bindgroup.eu/wp-content/uploads/2015/11/mrtool-v1.2.zip
dante.mantini@faber.kuleuven.be (Marco Ganzetti)Toolbox for spm12Multimodal mapping of brain structural properties by combining T1- and T2-weighted MR imaging data. A toolbox for the generation of the multimodal T1-w/T2-w ratio image.MRM - Multivariate and Repeated Measures
http://www.click2go.umip.com/i/software/mrm.html
martyn.mcfarquhar@manchester.ac.uk,shane.mckie@manchester.ac.uk (Martyn McFarquhar & Shane McKie)Toolbox for spm12A user-friendly MATLAB toolbox for group-level multimodal and repeated-measures models, using a multivariate GLM approach with permutation-based inference.NIRS-SPM
http://bispl.weebly.com/nirs-spm.html
shtak@kaist.ac.kr (Jong Chul Ye & Sungho Tak)Toolbox for spm5,spm8,spm12 NIRS-SPM is a statistical parametric mapping toolbox for near-infrared spectroscopy. Based on general linear model and Sun's tube formula, NIRS-SPM not only provides activation maps of oxy-, deoxy-, and total- hemoglobin, but also allows for the super-resolution activation localization.NS - Non-Stationary Cluster Extent Correction
http://fmri.wfubmc.edu/cms/software#NS
shayasak@wakehealth.edu (Satoru Hayasaka)Toolbox for spm2,spm5This toolbox implements the random field theory (RFT) version of cluster size inference under non-stationarity. Non-stationarity is particularly problematic in VBM (voxel-based morphometry) data, and a use of cluster p-values has been discouraged in analyses of such data. Uses code from Keith Worsley's FMRISTAT software. Also provides cluster p-values 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,spm8An 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,spm12This toolbox provides model-based 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 pre-processing 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 spm2Parallelized SPM2. Uses MPI to parallelize coregistration and reslicingREST - Resting-state fMRI data analysis toolkit
http://resting-fmri.sourceforge.net/
dawnwei.song@gmail.com,ycg.yan@gmail.com (Xiao-Wei Song & Chao-Gan Yan)Toolbox for spm99,spm2,spm5,spm8REST 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 spm5rfxplot 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 Weighted-least-squares
http://www.diedrichsenlab.org/imaging/robustWLS.html
jdiedric@uwo.ca,reza@bme.jhu.edu (Joern Diedrichsen & Reza Shadmehr)Toolbox for spm2,spm5,spm8,spm12This 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 EEG-fMRI
http://www.lni.hc.unicamp.br/~beltramini
gcbeltramini@gmail.com (Guilherme Coco Beltramini)Toolbox for spm8Straightforward 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 EEG-fMRI 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.SAMIT - Small Animal Molecular Imaging Toolbox
http://mic-umcg.github.io/samit/
samit@umcg.nl (David Vallez Garcia)Toolbox for spm8,spm12The aim of this toolbox is to facilitate the construction of new tracer specific templates and the subsequent voxel-based and/or volume-of-interest based analysis of small animal PET and SPECT brain images. The software is distributed with a T2-MRI rat template coregistered with the Paxinos anatomical atlas and several rat PET and SPECT templates.SCRalyze
http://scralyze.sourceforge.net/
d.bach@fil.ion.ucl.ac.uk (Dominik R. Bach)Toolbox for spm8Model-based 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,spm8Signed Differential Mapping is a statistical technique for meta-analyzing 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://www-personal.umich.edu/~rcwelsh/SimpleROIBuilder/
rcwelsh@med.umich.edu (Robert Welsh)Toolbox for spm2,spm5Creates 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,spm12Nonparametric permutation test for PET and second level fMRI data. Gives (familywise error rate) corrected p-values 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,spm5Adds 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://www-personal.umich.edu/~nichols/SPMd/
spmd-authors@umich.edu (Wen-Lin Luo & Thomas Nichols)Toolbox for spm99,spm2,spm5Allows 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
http://www.spmmouse.org/
sjs80@wbic.cam.ac.uk (Stephen Sawiak)Toolbox for spm5,spm8,spm12SPMMouse extends the functionality of SPM 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 (brain-extracted) image for use with the SPM results interface.SSM PCA - A multivariate toolbox for brain mapping analysis
http://feinsteinneuroscience.org/imaging-software
yma@nshs.edu,pspetsie@nshs.edu (Yilong Ma and Phoebe Spetsieris)Toolbox for spm99,spm2,spm5This 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.diedrichsenlab.org/imaging/suit.htm
jdiedric@uwo.ca (Joern Diedrichsen)Toolbox for spm8,spm12Improves the inter-subject normalization of infratentorial structures (cerebellum and brainstem). Contains a new high-resolution 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,spm5Suite of scripts that create surface-based renderings of SPM statistic mapsSwE - Sandwich Estimator Toolbox for Longitudinal & Repeated Measures Data
http://warwick.ac.uk/tenichols/software/SwE/
t.e.nichols@warwick.ac.uk (Bryan Guillaume & Thomas Nichols)Toolbox for spm8,spm12SwE is a toolbox to accommodate general repeated measures and longitudinal data. It makes no assumption about balanced designs and, through the use of a "marginal model", allows either between- or within-subject variables (e.g. in one longitudinal design, you can model both time and gender). Variance (& covariance) are estimated separately for each group. It has accurate parametric results that work reasonably well for at least 20 subjects per group, and otherwise a bootstrap resampling inference procedure (that additional provides FWE voxel- or cluster-wise inferences).TDT - The decoding toolbox
https://sites.google.com/site/tdtdecodingtoolbox/
tdt@bccn-berlin.de (Martin Hebart, Kai Gorgen)Toolbox for spm2,spm5,spm8,spm12The decoding toolbox is an easy to use, yet flexible software package for multivariate pattern analysis (MVPA) of functional and structural MRI data. TDT provides an interface to SPM which obviates the need to manually specify training and test samples and comes with a range of classifiers and feature selection schemes.Template-O-Matic toolbox
https://irc.cchmc.org/software/tom.php
christian.gaser@uni-jena.de (Christian Gaser, Marko Wilke, Mekibib Altaye, Scott Holland)Toolbox for spm5,spm8Using 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 5-18 years. It writes SPM2-compatible 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, spm12UF2C 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 spm2Toolbox for estimation and removal of movement-by-susceptibility 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.VarTbx - Variability Toolbox
http://douglasdgarrett.com/software
garrett@mpib-berlin.mpg.de (Stefan Schmidt & Douglas Garrett)Toolbox for spm8,spm12Measures within-voxel time series variability in fMRI data.Volumes Toolbox
http://sourceforge.net/projects/spmtools
volkmar.glauche@uniklinik-freiburg.de (Volkmar Glauche)Toolbox for spm2,spm5,spm8,spm12This 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.Wavelet-based Morphometry
http://www.wbmorphometry.com/
ejcanalesr@gmail.com (Erick J. Canales-Rodriguez)Toolbox for spm2,spm5,spm8Wavelet-based morphometry (WBM) is an alternative strategy to voxel-based 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.Wavelet-based SPM
http://miplab.epfl.ch/wspm/
Dimitri.VanDeVille@epfl.ch (Dimitri Van De Ville)Toolbox for spm2,spm5,spm8A 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,spm12This 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,spm12A viewing program for SPM. p-value 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/tools-catalog/xcede-spm-toolbox/
dbkeator@uci.edu (David Keator)Toolbox for spm2A 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. ASLtbx
http://www.cfn.upenn.edu/~zewang/ASLtbx.php
zewang@mail.med.upenn.edu (Ze Wang)Toolbox for spm8ASLtbx is a Matlab and SPM based toolkit for processing arterial spin labeling (ASL) perfusion MRI data. Current version is based on SPM8 though part of it may still work with SPM5 or 2. The function for quantifying cerebral blood flow should be SPM independent except the image reading and writing functions from SPM. In our website, you can find example ASL data acquired using PASL, CASL, or pseudo-CASL sequence. Customized scripts have been provided for each example dataset. Questions regarding ASL data processing or general ASL MRI can be posted in https://groups.google.com/forum/#!forum/asltbx-discussion-board.BENtbx
http://www.cfn.upenn.edu/~zewang/BENtbx.php
zewang@mail.med.upenn.edu (Ze Wang)Toolbox for spm8BENtbx (Brain Entropy Mapping Toolbox) is a Matlab and SPM based toolkit for brain entropy mapping using fMRI data. Entropy is calculated using Sample Entropy (SampEn). Because of the optimized SampEn calculation and C++ based implementation, a whole brain BEN mapping can be as fast as 3 seconds, compared to >7 hours using the included Matlab code. Sample data is provided in the same webpage.SVR-LSM toolbox
http://www.cfn.upenn.edu/~zewang/software.html
zewang@mail.med.upenn.edu (Ze Wang)Toolbox for spm8SVR-LSMtbx is a Matlab, libSVM, and SPM based toolkit for lesion-symptom mapping. Different from the voxel-based lesion-symptom mapping, SVR-LSM is multivariate. The detailed information can be found in our Human Brain Mapping paper. Sample lesion data and behavior data are provided to facilitate the use of SVR-LSM toolbox.AveLI
http://aveli.web.fc2.com/
info.aveli@gmail.com (Kayako Matsuo)Utility for spm5,spm8,spm12An easy-to-use MATLAB script to calculate the lateralization index of fMRI as described in Matsuo et al. J Neurosci Methods 2012.BrainMagix SPM Viewer
http://www.imagilys.com/brainmagix-spm-viewer/
info@imagilys.com (Imagilys)Utility for spm5,spm8A free, professional viewer for SPM fMRI activations. JAVA-programmed, cross-platform (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 user-friendly 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 spm99Windows program to convert Bruker to Analyze files.CBMG-Tools - Utilities for analysis, display, etc
http://www.brain.northwestern.edu/cbmg/cbmg-tools/
d-gitelman@northwestern.edu (Darren Gitelman)Utility for spm99Tools 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 cross-hairs hiding and DICOM conversion.Design Magic - Multicollinearity assessment for fMRI designs
http://www.matthijs-vink.com/tools.html
m.vink@azu.nl (Matthijs Vink)Utility for spm99,spm2Allows you to assess the multicollinearity in your fMRI-design 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 t-values will be. Also can calculate (and create) the most optimal high-pass filter for your design.dicom2nifti
http://www.aimfeld.ch/neurotools/neurotools.html
neurotools@aimfeld.ch (Adrian Imfeld)Utility for spm5,spm8dicom2nifti converts DICOM-files (.dcm) to NIfTI-files (.nii or .img/.hdr). A specified directory and its subdirectories are searched for DICOM-files. These files will then be converted to NIfTI format using SPM functions. The NIfTI-files will be properly named, moved to a target-directory and sorted in subdirectories according to their type (anatomical, functional, or DTI).Dynamic PET - Quantification of dynamic PET studies
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;590495cb.02
florian.wilke@rzbd.fh-hamburg.de,buchert@uke.uni-hamburg.de (Florian Wilke & Ralph Buchert)Utility for spm2Fully automated modeling of dynamic PET studies using the Ichise non-invasive plot. The toolbox, inclusive example dataset, is available via e-mail.Easy_ROI
http://www.sbirc.ed.ac.uk/LCL/LCL_M1.html
cyril.pernet@ed.ac.uk (Cyril Pernet)Utility for spm2,spm5,spm8Reads 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,spm8Returns the number of voxels and the volume of segmented modulated 3D volumes (GM, WM or CSF).FDRill - Plot T image histogram and FDR PP-plot
http://www-personal.umich.edu/~nichols/FDR/FDRill.m
nichols@umich.edu (Tom Nichols)Utility for spm2For a given T image plots the histogram (root-o-gram, actually) and the log-log P-P plot, which illustrates how the FDR threshold is found. Can be used interactively or scripted.Fluctuation - Task-independent connectivity discussion group
http://www.nitrc.org/projects/fluctuations
handwerkerd@mail.nih.gov (Daniel Handwerker)Utility for spm99,spm2,spm5Discussion 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 non-neural 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 spm99MATLAB functions for visualization, time series extraction, and trial averaging. C programs for slice timing correction, ASL sync-subtraction, 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 spm2A database representing normal fractional anisotropy values for the age (20-69 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,spm8Optimizes 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 spm99Create 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)Toolbox for spm8Implements multiple algorithms for ICA of group (and single subject) fMRI data. JG - John's Gems
http://www-personal.umich.edu/~nichols/JohnsGems.html
john@fil.ion.ucl.ac.uk (John Ashburner)Utility for spm99,spm2,spm5Essential 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 spm99Converts 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,spm8log_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,spm8Detrend fMRI time-series 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):360-6.MatlabTFCE - Standalone MATLAB implementation of permutation TFCE correction
https://github.com/markallenthornton/MatlabTFCE
mthornton@fas.harvard.edu (Mark Thornton)Utility for This package offers a standalone implementation of multiple comparison correction for fMRI data. It achieves this through a permutation testing approach which controls familywise error rate by comparing voxelwise statistics to the maximal statistics obtained from repeating the analysis with randomized data. This maximal permuted statistic correction technique is combined with the threshold free cluster enhancement (TFCE) transformation due to Smith & Nichols (2009), which obviates the need for arbitrary voxelwise cluster-forming thresholds and instead produces continuous correct p-values for all voxels.Motion Fingerprint
http://www.medizin.uni-tuebingen.de/kinder/en/research/neuroimaging/software/
Marko.Wilke@med.uni-tuebingen.de (Marko Wilke)Utility for spm8,spm12Allows 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 usemri_toolbox - Analyze read/write utilities
http://eeg.sourceforge.net
Darren.Weber@radiology.ucsf.edu (Darren Weber)Utility for spm99A 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,spm5Visualization 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@uniklinik-freiburg.de (Volkmar Glauche)Utility for spm2,spm5Plug in for SPM's spm_orthviews (accessed from "Check Reg" button). From pop-up menu can reorient, visualize diffusion tensors, use a movie tool to step through slices or create ROI masks.PCT - Percent Change Threshold
http://www-personal.umich.edu/~nichols/PCT/
nichols@umich.edu (Thomas Nichols)Utility for spm99Re-expresses 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@mrc-cbu.cam.ac.uk (Matthew Brett)Utility for spm99Converts 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,spm5Automatically batch-converts 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.dyndns.org/SEM.htm
d.steele@dundee.ac.uk (Douglas Steele)Utility for spm99,spm2,spm5,spm8Allows 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.mrc-cbu.cam.ac.uk/imaging/DisplaySlices
matthew.brett@mrc-cbu.cam.ac.uk (Matthew Brett)Utility for spm2Shows 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@uniklinik-freiburg.de (Matthew Brett, Volkmar Glauche)Utility for spm2,spm5,spm8,spm12Computes 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,spm5Visualization 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,spm8This toolbox implements the iterative Two-Threshold (iTT) approach to correct height thresholds in SPM.VBMtools - Collection of scripts and hints for VBM
http://dbm.neuro.uni-jena.de/vbm/
christian.gaser@uni-jena.de (Christian Gaser)Utility for spm2,spm5,spm8A collection of extensions to the segmentation algorithm of SPM2, SPM5 and SPM8 to provide voxel-based morphometry (VBM). Includes regularized segmentation and longitudinal anlayses.vis - SPM image visualization
http://tools.robjellis.net
robjellis@gmail.com (Rob Ellis)Utility for spm5,spm8Utility 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 spm99Converts SIEMENS Vision ACR-NEMA 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 spm99Analyzes 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,spm8An easy-to-use 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 spm5AutoSPET (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 pre-processing/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 spm8Once 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 (pre-processing, 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 spm99Automate fMRI data post processing.parallelize_matlabbatch
http://algoholic.eu/parallelize_matlabbatch/
s.adaszewski@gmail.com (Stanislaw Adaszewski)UtilityBatch utility for spm8This 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,spm5A 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. SPMJobs12
http://zhupsy.com/more
jerryzhu@siu.edu (Jerry Zhu)UtilityBatch utility for spm12Batch process multiple subjects' fMRI data by running a single command up to the first level analysis; separate files into each processing step; generate job files beforehand for you to double-check and review; save informative graphs as pdf for quality control; can send email notification when a job is done.spm2-batch
http://spm2-batch.sourceforge.net/
S.F.W.Neggers@fss.uu.nl (Bas Neggers)UtilityBatch utility for spm2Batch 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 spm2A batch system SPM2, including command-line specification of slice_timing options. Tested on Matlab 6.1 & 6.5.spm2Batch
http://www-personal.umich.edu/~rcwelsh/spm2Batch/
rcwelsh@med.umich.edu (Robert Welsh)UtilityBatch utility for spm2Batch 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,spm8spmbatch (former spm5batch) creates and runs SPM-jobs for multiple subjects by replacing paths in a given template-job. Jobs on the first level (single subject) are supported, e.g. preprocessing of fMRI data, first-level statistics, image calculator, check registration, jobs with external SPM toolboxes.spmjob
http://sourceforge.net/projects/spmjob/
tanner@gmx.de (Thomas Tanner)UtilityBatch utility for spm2A wrapper for the SPM2 batch interface which provides a GUI for setting all parameters. Supports pre-processing, parameter estimation, contrasts and second level analysis. spmjob has both flexible scripting support and a user friendly GUI.X_batch
http://x-batch.sourceforge.net
biostr@users.sourceforge.net (Xenia Hertzenberg)UtilityBatch utility for spm2Integrates 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 spm2Batch processing system for SPM2. Note, contains raw-data 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 spm99T1-weighted MRI template based on 9 normal baboons, and PET template based on [15-O]water PET images of 7 baboons.Brain Atlases of 2-year-olds
http://www.brain-development.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 T1-weighted MRI scans (1mm isotropic resolution) of 20 healthy young participants.CCHMC Pediatric Atlas
http://www.irc.cchmc.org/software/pedbrain.php
Marko.Wilke@med.uni-tuebingen.de (Marko Wilke)Templates for spm99,spm2GM and WM template defined with 200 children aged 5 to 18. Created for SPM99 but SPM2 compatible (for SPM5, use the Template-O-Matic toolbox listed above).Dementia-Specific [18F]-FDG-PET template for SPM normalization
http://155.253.6.176/inlab/PET_template.php
pasqualeanthony.dellarosa@gmail.com,perani.daniela@hsr.it (Pasquale Anthony Della Rosa & Daniela Perani)Templates for spm99,spm2,spm5,spm8,spm12The Dementia-Specific [18F]-FDG-PET template (after spatial normalization of [18F]-FDG-PET 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).Ovine Brain Atlas
https://www.mcgill.ca/bic/resources/brain-atlases/ovine-brain-atlas
bjoern.nitzsche@izi.fraunhofer.de (Bjorn Nitzsche)Templates for The ovine, unbiased, population-averaged standard magnetic resonance imaging template brain volume: a common stereotaxic reference frame to localize anatomical and functional information. We have used t1w MRI volumes from a group of 14 normal adult sheep to create the template and a priori probability of cerebral gray (GM) and white (WM) matter as well as cerebrospinalfluid (CSF). Nonlinear normalization of numerous sheep brains were mapped to an average template image. See Nitzsche et al, Frontiers in Neuroanatomy, 2015, for more details.Template images for neuroimaging in Macaca fascicularis
http://purl.org/net/kbmd/cyno
kevin@wustl.edu (Kevin Black)Templates for spm99T1-weighted MRI template based on 11 normal cynomolgus monkeys.MRI template of Macaca Fascicularis Brain
http://www.cima.es/labs-en/instrumental-techniques-micropet/technologies/1
eprietoaz@unav.es (Maria Collantes & Elena Prieto )Templates for T1-weighted MRI, 18F-DOPA PET and 11C-DTBZ PET templates based on 15 healthy Macaca Fascicularis subjects, available in Analyze format.112RM-SL template images for neuroimaging in rhesus macaque (Macaca mulatta)
http://brainmap.wisc.edu/monkey.html
dm10@medicine.wisc.edu (Donald McLaren)Templates for spm5,spm8T1-weighted MRI template based on 112 adult Macaca mulattas (30 females), tissue priors, and T2-weighted 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 spm99T1-weighted MRI template based on 11 normal nemestrinas, and PET template based on [15-O]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 Sprague-Dawley rats.18F-DOPA and 123I-FP-CIT human templates for SPM normalisation
http://www.nitrc.org/projects/spmtemplates
javier191185@gmail.com (Garcia-Gomez F.J., Garcia-Solis D.)Templates for spm5,spm818F-DOPA PET template (after spatial normalization of T1-weighted MRI images) from 10 healthy humans, and 123I-FP-CIT SPECT template from 26 healthy humans.UNC 0-1-2 Infant Atlases
http://www.nitrc.org/projects/pediatricatlas
fengshi@med.unc.edu (Feng Shi)Templates for There are 3 atlases dedicated for neonates (T2), 1-year-olds (T1), and 2-year-olds (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/bio-imaging-lab/research/mri-atlases/zebra-finch-brain-atlas/
colline.poirier@ua.ac.be (Colline Poirier)Templates for spm99,spm2Three-dimensional MRI atlas of the zebra finch brain, available in Analyze format.