Many SPM users have created tools for neuroimaging analyses that are based on SPM. You will find here a list of these tools classified between Toolboxes, Utilities, Batch Systems and Templates. The distinction between Toolboxes and Utilities can be blurry, but for the purposes of this page we define a toolbox to be a utility that can be completely operated via a graphical user interface.

If you notice inaccuracies or out of date links, please email the SPM manager. Likewise, to have your SPM extension linked here, send an email including a URL, a contact email, and a brief summary (please note if any MATLAB toolboxes are required, or if it is platform-specific).

The SPM Developers take no responsibility for the usability of the extensions listed here. In particular, some extensions may be mutually incompatible. Please contact the respective extension authors with questions and problems (though CC'ing answered questions to the Email list will be appreciated).

Extensions compatible with SPM8, SPM5, SPM2, SPM99.

The list of SPM extensions is also available as an RSS feed.

Note: All email addresses in this page have their "@" replaced with "_at_" to minimize spam. Please reverse this change before emailing.

AQuA | AAL | ACID | ALVIN | ArtRepair | AMAT | AnalyzeMovie | Anatomy | aslm | ASLtbx | at4fmri | aws4SPM | BrainNetViewer | BredeQuery | CCAfMRI | CLASS | Clinical | Complexity | conn | ConnExT | CPCA | DAiSS | DICOMCD_Import | Diffusion_II | Distance | DPARSF | DRIFTER | EMS | ExtractVals | FASL | FAST | fECM | FDR | FieldMap | fieldmap_undistort | FieldTrip | fMRIPower | fOSA | Grocer | HV | IBASPM | iBrainAT | iBrainLT | INRIAlign | IBZM_tool | ISAS | LI | LogTransform | MARINA | MarsBar | MASCOI | mfBox | Masking | Masks | MIP-C | MM | multifocal | NIRS-SPM | NS | Ortho | PhysIO | PSPM | REST | rfxplot | RobustWLS | SAfE | SCRalyze | SDM | SimpleROIBuilder | SnPM | spm_wavelet | SPMd | SPMMouse | SSM | SUIT | SurfRend | TOM | UF2C | Unwarp2 | Volumes | WBM | WSPM | WFU_PickAtlas | xjView | XMLTools

AveLI | BrainMagix | Bruker2Analyze | CBMG-Tools | Design_Magic | dicom2nifti | DynPET | Easy_ROI | Easy_Volumes | FDRill | Fluctuation | fToolbelt | FAD | GA | GE2SPM | GIFT | JG | L2S | log_roi_batch | LMGS | Motion | mri_toolbox | MSU | Orth1 | PCT | pvconv | r2agui | SEM | slice_overlay | TSDiffAna | TSU | iTT | VBMtools | VIS | visionToSPM | VoiTool

aa | AutoSPET | BatchAAL | KULscripts | parallelize_matlabbatch | spm_segment | spm2-batch | spm2batch | spm2Batch | spmbatch | spmjob | X_batch | zephyr

Baboon | BrainDev_Atlas | Cerebellum | CCHMC_Pediatric | Dementia_PET | Macaca_Fascicularis | Macaca_Fascicularis_PET | Macaca_Mulatta | Macaca_Nemestrina | Rat | SPMtemplates | UNC_Pediatric | Zebra_Finch

**Summary**: 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.

**Summary**: Automated parcellation method, as described in Tzourio-Mazoyer et al. NI 2002.

**Author**: Cyceron

**Summary**: The 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.

**Author**: Siawoosh Mohammadi

**Summary**: Segmentation of the lateral ventricles validated in infants, adults and patients with Alzheimer's disease. Works with both T1 and T2 images.

**Author**: Matthew Kempton

**Summary**: 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.

**Author**: Paul Mazaika

**URL**: http://cibsr.stanford.edu/tools/human-brain-project/artrepair-software.html

**Summary**: 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?

**Author**: Antonia Hamilton

**Summary**: Create AVI movies from Analyze images, of axial, coronal, sagittal or ortho slices. Requires Matlab6 or greater.

**Author**: Robert Welsh

**Summary**: This 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.

**Author**: Simon Eickhoff

**URL**: http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html

**Summary**: aslm is an object orientated toolbox for common tasks associated with the analysis of arterial spin labeling (ASL) and other MRI data.

**Author**: Philipp Homan

**Summary**: 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 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.

**Author**: Ze Wang

**Summary**: Allow 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.

**Summary**: Structural adaptive smoothing fMRI data as described in Tabelow et al. NI (2006).

**Summary**: 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.

**Author**: Mingrui Xia

**Summary**: BredeQuery 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).

**Author**: Bartlomiej Wilkowski

**Summary**: The 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.

**Author**: Magnus Borga

**Summary**: Multivariate 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).

**Author**: Ged Ridgway

**URL**: Contact email above

**Summary**: 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.

**Author**: Rorden, Bonilha, Fridriksson, Bender and Karnath

**URL**: http://www.mccauslandcenter.sc.edu/CRNL/clinical-toolbox

**Summary**: Complexity 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.

**Author**: Anitha Priya Krishnan, Jun Fang, Robert Smith, Danny JJ Wang

**Summary**: Performs 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.

**Author**: Alfonso Nieto-Castanon

**Summary**: 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.

**Author**: Guilherme Coco Beltramini

**Summary**: 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.

**Author**: Todd Woodward

**Summary**: SPM12 toolbox for Data Analysis in Source Space (beamforming, minimum norm and related methods), developed by collaboration of UCL, Oxford and other MEG centres.

**Author**: Vladimir Litvak

**Summary**: 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.

**Author**: Pieter Vandemaele

**Summary**: Post-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.

**Author**: Volkmar Glauche

**Summary**: This toolbox features two independent modules: 1) tools for group homogeneity diagnosis using pairwise distances; 2) non-parametric random-effect analysis using permutation tests. The permutation testing module is platform-specific: both Windows and 32-bit Linux are currently supported. On other systems, a re-compilation is needed (see instructions from the URL).

**Author**: Sébastien Mériaux, Alexis Roche, Ferath Kherif, & Bertrand Thirion

**Summary**: DPARSF 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.

**Author**: Chao-Gan Yan

**Summary**: 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 respiration-induced noise, and then eliminate them from the brain data. The toolbox can be operated both in graphical and batch mode.

**Author**: Arno Solin and Simo Sarkka

**Summary**: Fully 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.

**Author**: Koen Van Leemput

**Summary**: Given a ROI binary mask image, this toolbox will extract values and report mean and variance.

**Author**: Robert Welsh

**Summary**: 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.

**Author**: Luis Hernandez

**Summary**: FAST 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.

**Author**: Jessica Schrouff, Dorothee Coppieters & Christophe Phillips

**Summary**: 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 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).

**Author**: Alle Meije Wink

**URL**: https://github.com/amwink/bias/tree/master/matlab/fastECM

**Summary**: Adds FDR-corrected p-values and thresholds to SPM99 results page

**Author**: Thomas Nichols

**Summary**: Toolbox for creating unwrapped field maps and unwarping EPI. Note that for SPM5 and above, the FieldMap Toolbox is part of the SPM distribution.

**Author**: Jesper Andersson & Chloe Hutton

**Summary**: Uses a measured field map to undistort EPI images.

**Author**: Rhodri Cusack

**Summary**: 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 time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing.

**Author**: Robert Oostenveld

**Summary**: This 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.

**Author**: Jeanette Mumford

**Summary**: fOSA is a software package for the processing and analysis of functional neuroimaging data using Near Infrared Spectroscopy (NIRS).

**Author**: Peck Hui Koh

**URL**: http://www.ucl.ac.uk/medphys/research/borl/nirs/nirs/current_projects/funct_softdev/fosa

**Summary**: 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.

**Summary**: HV is a SPM toolbox fully integrated into the SPM8 GUI to calculate hippocampal volumes based on 3D MPRAGE images.

**Author**: jung diagnostics GmbH

**Summary**: 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.

**Summary**: The 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.

**Author**: David Abbott

**Summary**: The 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.

**Author**: David Abbott

**Summary**: A 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.

**Author**: Alexis Roche

**URL**: http://www-sop.inria.fr/epidaure/Collaborations/IRMf/INRIAlign.html

**Summary**: 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, VOI-analysis of striatal IBZM uptake, classification of striatal IBZM-uptake, and standardized display.

**Author**: Florian Wilke

**Summary**: ISAS 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.

**Author**: Hal Blumenfeld

**Summary**: Allows assessment of laterality effects in imaging data using various thresholding options. Amog 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. The latest version requires spm8 (contact Marko for earlier versions).

**Author**: Marko Wilke

**URL**: http://www.medizin.uni-tuebingen.de/kinder/en/research/neuroimaging/software/

**Summary**: Toolbox 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.

**Author**: Dave Langers

**Summary**: 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 Tzourio-Mazoyer et al. (2002). Voxel coordinates of brain structures come from their SPM toolbox AAL (automated anatomical labeling).

**Author**: Bertram Walter

**Summary**: 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.

**Author**: Matthew Brett

**Summary**: Explores 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).

**Author**: Matthias Reimold

**URL**: http://homepages.uni-tuebingen.de/matthias.reimold/mascoi/

**Summary**: For 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.

**Summary**: 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.

**Author**: Ged Ridgway

**Summary**: An 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.

**Author**: Leighton Barnden

**URL**: http://www.anzsnm.org.au/cms/specialisations/software/spm-toolboxes/

**Summary**: MIP-C is a simple program that creates a color image with the maximum intensity projection on a glass brain in three orthogonal planes.

**Author**: Guilherme Coco Beltramini

**Summary**: 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.

**Author**: Ferath Kherif

**URL**: Contact email above

**Summary**: 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 (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.

**Author**: Simo Vanni

**Summary**: 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.

**Author**: Jong Chul Ye & Sungho Tak

**Summary**: This 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).

**Author**: Satoru Hayasaka

**Summary**: 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)

**Author**: Luis Hernandez

**Summary**: This 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").

**Author**: Lars Kasper

**URL**: http://www.translationalneuromodeling.org/documentation/

**Summary**: Parallelized SPM2. Uses MPI to parallelize coregistration and reslicing

**Author**: Jejo Koola

**Summary**: 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).

**Author**: Xiao-Wei Song & Chao-Gan Yan

**Summary**: 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.

**Author**: Jan Glascher

**Summary**: 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.

**Author**: Joern Diedrichsen & Reza Shadmehr

**URL**: http://www.icn.ucl.ac.uk/motorcontrol/imaging/robustWLS.html

**Summary**: 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 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.

**Author**: Guilherme Coco Beltramini

**Summary**: Model-based analysis for peripheral psychophysiological signals (e.g. skin conductance) including GLM and DCM.

**Author**: Dominik R. Bach

**Summary**: Signed 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.

**Author**: Joaquim Radua

**Summary**: Creates mask images based on spheres or boxes.

**Author**: Robert Welsh

**URL**: http://www-personal.umich.edu/~rcwelsh/SimpleROIBuilder/

**Summary**: Nonparametric permutation test for PET and second level fMRI data. Gives (familywise error rate) corrected p-values that do not depend on random field theory.

**Author**: Andrew Holmes & Thomas Nichols

**Summary**: 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.

**Author**: Alle Meije Wink

**URL**: http://fs2.psychiatry.cam.ac.uk/~amw71/publications/TMI2004/TMI2004_software.html

**Summary**: 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.

**Author**: Wen-Lin Luo & Thomas Nichols

**Summary**: 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 (brain-extracted) image for use with the SPM results interface.

**Author**: Stephen Sawiak

**Summary**: 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.

**Author**: Yilong Ma and Phoebe Spetsieris

**Summary**: Improves 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.

**Author**: Joern Diedrichsen

**Summary**: Suite of scripts that create surface-based renderings of SPM statistic maps

**Author**: Itamar Kahn

**Summary**: 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 5-18 years. It writes SPM2-compatible data and now includes an option to generate customized priors for "new segment".

**Author**: Christian Gaser, Marko Wilke, Mekibib Altaye, Scott Holland

**Summary**: 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.

**Author**: Brunno M. Campos

**Summary**: Toolbox 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.

**Author**: Jesper Andersson & Chloe Hutton

**Summary**: 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.

**Author**: Volkmar Glauche

**Summary**: Wavelet-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.

**Author**: Erick J. Canales-Rodriguez

**Summary**: 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.

**Author**: Dimitri Van De Ville

**Summary**: 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.

**Author**: Joseph Maldjian

**Summary**: A 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.

**Author**: Xu Cui, Jian Li, Xiaowei Song

**Summary**: 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.

**Author**: David Keator

**URL**: http://www.birncommunity.org/tools-catalog/xcede-spm-toolbox/

**Summary**: An easy-to-use MATLAB script to calculate the laterality index of fMRI as described in Matsuo et al. J Neurosci Methods 2012.

**Author**: Kayako Matsuo

**Summary**: A 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.

**Author**: Imagilys

**Summary**: Windows program to convert Bruker to Analyze files.

**Author**: Chris Rorden

**URL**: http://www.mccauslandcenter.sc.edu/mricro/mricro/bru2anz/index.html

**Summary**: 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 cross-hairs hiding and DICOM conversion.

**Author**: Darren Gitelman

**Summary**: Allows 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.

**Author**: Matthijs Vink

**Summary**: dicom2nifti 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).

**Author**: Adrian Imfeld

**Summary**: Fully automated modeling of dynamic PET studies using the Ichise non-invasive plot. The toolbox, inclusive example dataset, is available via e-mail.

**Author**: Florian Wilke & Ralph Buchert

**URL**: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;590495cb.02

**Summary**: Reads and returns data of any images from a region of interest identified within the SPM result table.

**Author**: Cyril Pernet

**Summary**: Returns the number of voxels and the volume of segmented modulated 3D volumes (GM, WM or CSF).

**Author**: Cyril Pernet

**Summary**: For 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.

**Author**: Tom Nichols

**Summary**: 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 non-neural fluctuations, and applications to clinical populations.

**Author**: Daniel Handwerker

**Summary**: MATLAB 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.

**Author**: Luis Hernandez

**URL**: http://web.eecs.umich.edu/~hernan/Public/Programs/Mfiles/

**Summary**: A database representing normal fractional anisotropy values for the age (20-69 years) and sex of individual.

**Author**: Khin Khin Tha

**Summary**: Optimizes event related fMRI designs by statistical and psychological criterion. (Matlab Signal Processing Toolbox required).

**Author**: Tor Wager

**URL**: http://www.columbia.edu/cu/psychology/tor/genetic_algorithms.html

**Summary**: Create SPM compatible Analyze images, including the .mat file to relate image coordinates to scanner coordinates.

**Author**: Souheil Inati

**URL**: http://web.archive.org/web/20030622131151/http://dbic.dartmouth.edu/~inati/tools/ge2spm.php

**Summary**: Implements multiple algorithms for ICA of group (and single subject) fMRI data.

**Author**: Vince Calhoun

**Summary**: 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.

**Author**: John Ashburner

**Summary**: Converts output data from LORETA into SPM compatible format.

**Author**: Sergey Pakhomov

**Summary**: 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.

**Author**: Adrian Imfeld

**Summary**: Detrend 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.

**Author**: Paul Macey

**Summary**: 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

**Author**: Marko Wilke

**URL**: http://www.medizin.uni-tuebingen.de/kinder/en/research/neuroimaging/software/

**Summary**: 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.

**Author**: Darren Weber

**Summary**: Visualization of SPM99 clusters in terms of Talairach Daemon anatomical region labels, but converting MNI coordinates of data to Talairach coordinates.

**Author**: Sergey Pakhomov

**Summary**: Plug 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.

**Author**: Volkmar Glauche

**Summary**: Re-expresses standard deviation in useful units, the minimum percent change required to obtain a significant result.

**Author**: Thomas Nichols

**Summary**: Converts Bruker format MRI data to Analyze or MINC image format; based on converters by Andrew Janke (MINCtools).

**Author**: Matthew Brett

**Summary**: Automatically 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/

**Author**: Bas Neggers

**Summary**: Allows a MATLAB based Structural Equation Modelling (SEM) calculation for fMRI data. An example is used to illustrate potential pitfalls and solutions.

**Author**: Douglas Steele

**Summary**: 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.

**Author**: Matthew Brett

**Summary**: 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.

**Author**: Matthew Brett, Volkmar Glauche

**Summary**: Visualization of SPM99 clusters on Talairach atlas sections.

**Author**: Sergey Pakhomov

**Summary**: This toolbox implements the iterative Two-Threshold (iTT) approach to correct height thresholds in SPM.

**Author**: Tibor Auer

**URL**: http://www.biomednmr.mpg.de/index.php?option=com_content&task=view&id=37&Itemid=43

**Summary**: A collection of extensions to the segmentation algorithm of SPM2, SPM5 and SPM8 to provide voxel-based morphometry (VBM). Includes regularized segmentation and longitudinal anlayses.

**Author**: Christian Gaser

**Summary**: 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.

**Author**: Rob Ellis

**Summary**: Converts SIEMENS Vision ACR-NEMA files (*.ima) to SPM Analyze, in particular preserving the orientation/position information.

**Author**: Sebastian Thees

**URL**: http://www.charite.de/ch/neuro/forschung/teams/klinisch/people/thees/thees_frameset.htm

**Summary**: Analyzes VOIs, including predifined Talairach VOIs, mask image saving and ascii data output.

**Author**: Sergey Pakhomov

**Summary**: An 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.

**Author**: Rhodri Cusack

**Summary**: 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 pre-processing/statistics and ending finally with the running of the algorithm of classification of obtaining files mdata.

**Author**: Pierangelo Veltri et al.

**Summary**: 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 (pre-processing, first level, results and labeling). The batch script can be evoked from spm8 batch interface. In batch interface: SPM > Tools > AAL.

**Author**: Atesh Koul

**URL**: https://github.com/ateshkoul/NeuroImaging/tree/master/spm/batch_aal

**Summary**: Automate fMRI data post processing.

**Author**: Stefan Sunaert & Erik Beatse

**URL**: http://www.kuleuven.ac.be/radiology/Research/fMRI/kulSPM/

**Summary**: 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.

**Author**: Stanislaw Adaszewski

**Summary**: 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.

**Author**: Jon Jackson

**Summary**: 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.

**Author**: Bas Neggers

**Summary**: A batch system SPM2, including command-line specification of slice_timing options. Tested on Matlab 6.1 & 6.5.

**Author**: Jejo Koola

**Summary**: 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.

**Author**: Robert Welsh

**Summary**: spmbatch (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.

**Author**: Adrian Imfeld

**Summary**: A 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.

**Author**: Thomas Tanner

**Summary**: Integrates Protege ontology and SPM2 batch processing utility. It does both the preprocessing and stats, though not the results.

**Author**: Xenia Hertzenberg

**Summary**: Batch processing system for SPM2. Note, contains raw-data conversion function which will need to be modified for other sites.

**Author**: Craig Bennett

**Summary**: T1-weighted MRI template based on 9 normal baboons, and PET template based on [15-O]water PET images of 7 baboons.

**Author**: Kevin Black

**Summary**: 33 brain atlases of two year old subjects, of 83 regions each, together with their related MRIs

**Author**: Daniel Rueckert

**Summary**: 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.

**Author**: Joern Diedrichsen

**URL**: http://www.icn.ucl.ac.uk/motorcontrol/imaging/propatlas.htm

**Summary**: GM 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).

**Author**: Marko Wilke

**Summary**: The 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).

**Summary**: T1-weighted MRI template based on 11 normal cynomolgus monkeys.

**Author**: Kevin Black

**Summary**: T1-weighted MRI, 18F-DOPA PET and 11C-DTBZ PET templates based on 15 healthy Macaca Fascicularis subjects, available in Analyze format.

**Author**: Maria Collantes & Elena Prieto

**URL**: http://www.cima.es/labs-en/instrumental-techniques-micropet/technologies/1

**Summary**: T1-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.

**Author**: Donald McLaren

**Summary**: T1-weighted MRI template based on 11 normal nemestrinas, and PET template based on [15-O]water PET images from 9 of the 11.

**Author**: Kevin Black

**Summary**: "Paxinos space" rat template based on five adult female Sprague-Dawley rats.

**Author**: Christian Spengere

**Summary**: 18F-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.

**Summary**: 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.

**Author**: Feng Shi

**Summary**: Three-dimensional MRI atlas of the zebra finch brain, available in Analyze format.

**Author**: Colline Poirier

**URL**: https://www.uantwerpen.be/en/rg/bio-imaging-lab/research/mri-atlases/zebra-finch-brain-atlas/