By members & collaborators of the Wellcome Trust Centre for Neuroimaging
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If you notice inaccuracies or out of date links, please email the SPM manager.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).
Finn Aarup Nielsen's Bibliography on Neuroinformatics and the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) are also useful references.
Extensions known to be compatible with SPM8 are marked with "SPM8".
Extensions known to be compatible with SPM5 are marked with "SPM5".
Extensions known to be compatible with SPM2 are marked with "SPM2".
Extensions known to be compatible with SPM99 are marked with "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 | ArtRepair | AMAT | AnalyzeMovie | Anatomy | aws4SPM | BredeQuery | CCAfMRI | conn | DICOMCD_Import | Diffusion_II | Distance | EMS | ExtractVals | FAST | FieldMap | FDR | fieldmap_undistort | FieldTrip | fOSA | HRF | IBASPM | INRIAlign | IBZM_tool | ISAS | LI | MARINA | MarsBar | MASCOI | mfBox | Masking | Masks | MM | multifocal | NIRS-SPM | NS | orthTS | PSPM | REST | RobustWLS | SimpleROIBuilder | SDM | SnPM | spm_wavelet | SPMd | SPMMouse | SSM | SUIT | SurfRend | TOM | Unwarp2 | Volumes | WSPM | WFU_PickAtlas | xjView | XMLTools
ArtifactRepair | Bruker2Analyze | CBMG-Tools | Design_Magic | dicom2nifti | DynPET | Easy_ROI | Easy_Volumes | FDRill | Fluctuation | fToolbelt | FAD | GA | GE2SPM | GIFT | JG | L2S | log_roi_batch | LMGS | minc2analyze | MINCtools | mri_toolbox | MSU | Orth1 | PCT | pvconv | r2agui | SEM | slice_overlay | TSDiffAna | TSU | TT | VBMtools | visionToSPM | VoiTool
aa | AutoSPM2 | ezspm2 | FixBatch | KF-Batch | KULscripts | spm_batch | SPM_Script | spm_segment | spm2-batch | spm2batch | spm2Batch | spm2batchJJ | spmbatch | spmjob | X_batch | zephyr
Rhesus-Macaque | Template-Karolinska | Template-cyno | Template-N2K | Template-B2K | Template-Macaca | Template-CCHMCped | Brain-Atlases-2year | Cerebellum | Zebra
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
URL: http://www.cyceron.fr/web/aal__anatomical_automatic_labeling.html
Summary: Enhanced version of previous ArtifactRepair utility, includes motion outliers, improved estimation, and validation of repairs for every subject. Demonstrated large estimation accuracy improvements for severe motion (5+ mm) fMRI data sets from FraX syndrome and other patients.
Author: Paul Mazaika and Susan Whitfield-Gabrieli
URL: http://cibsr.stanford.edu/tools/ArtRepair/ArtRepair.htm
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
Summary: Structural adaptive smoothing fMRI data as described in Tabelow et al. NI (2006).
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: 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: 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 in SPM2. 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: 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: 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.
Summary: Toolbox for creating unwrapped field maps and unwarping EPI. This toolbox is now part of SPM5.
Author: Jesper Andersson & Chloe Hutton
Summary: Adds FDR-corrected p-values and thresholds to SPM99 results page
Author: Thomas Nichols
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: 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.medphys.ucl.ac.uk/research/nirs/software_fosa.html
Summary: Implements a Bayesian estimation of the haemodynamic response that finds a tradeoff between physiological constraints and the information given by the data. Can handle trend estimation, non synchronous paradigm, multiple sessions...
Author: Philippe Ciuciu
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: 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, allowing for unattended analyses. Matlab from version 6.5.1 on is required.
Author: Marko Wilke
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/servlet/NM?command=downloadResource&resourceID=298
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: GUI for a set of time series extraction programs which allows you at your time series data with minimal processing, just a little filtering and event averaging. Can operate independently of SPM.
Author: Luis Hernandez
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: 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
Summary: Creates mask images based on spheres or boxes.
Author: Robert Welsh
URL: http://www-personal.umich.edu/~rcwelsh/SimpleROIBuilder
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: 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. Also writes SPM2-compatible data.
Author: Marko Wilke
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. This toolbox is now part of SPM5.
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: 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
Summary: Software tools to visually review fMRI data, automatically detect and repair volume and slice artifacts, and automatically remove spike noise. Documentation includes artifact examples and a sample protocol. (mostly SPM99 compatible)
Summary: Windows program to convert Bruker to Analyze files.
Author: Chris Rorden
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: http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0204&L=spm&P=R6731
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://www.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: Impliments 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: Functions (spm_vol_minc.m, spm_write_4dvol.m) to help convert 3D and 4D MINC files to analyze files.
Author: Satrajit Ghosh
Summary: Various programs to convert, interrogate and manipulate MINC images. Includes Analyze and Bruker Paravision to MINC converter.
Author: Andrew Janke
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 SPM2'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
URL: http://www.dundee.ac.uk/cmdn/staff/douglas_steele/structural_equation_modelling
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
URL: http://www.mrc-cbu.cam.ac.uk/Imaging/Common/display_slices.shtml
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 Two-Threshold (TT) 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 and SPM5 to support voxel-based morphometry (VBM). Includes regularized segmentation and longitudinal anlayses.
Author: Christian Gaser
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. Versions currently available for: (1) Siemens data, SPM5 & NIFTI; (2) Bruker, SPM2 & Analyze.
Author: Rhodri Cusack
Summary: As motivated for surgical planning, AutoSPM consists of an user-friendly graphical user interface and automation scripts that reduce the user interaction time to less than five minutes.
Author: Imagilys
Summary: ezSPM2 is a graphical user interface (GUI) for the automatic processing of functional imaging data with SPM2.
Author: Ralph Schnitker & Jochen Weber
Summary: SPM5 Batch scripts for create preprocessing and modeling job files for SPM5, allowing one to avoid entering all of the scans manually.
Author: Steve Fix
URL: http://www.ling.northwestern.edu/~fix/SPM5_batch_main_page.html
Summary: Unlike many other batching utilities, this one provides batch scripting of SPM results. Available as attachment to SPM help email.
Author: Ferath Kherif
URL: http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind04&L=SPM&P=R323755
Summary: Automate fMRI data post processing.
Author: Stefan Sunaert & Erik Beatse
URL: http://www.kuleuven.ac.be/radiology/Research/fMRI/kulSPM
Summary: To make make the spm-batch feature accessible to non-programmers. (Only works on Windows; could work on Unix with minor modifications).
Author: Sebastian Thees
URL: http://www.charite.de/ch/neuro/forschung/teams/klinisch/people/thees/spm_batch-download.htm
Summary: Offers a batch system for the fMRI analysis; reduces tedious SPM interaction, provides an fMRI parameter plausibility check facility and does intensive run-time logging and reporting.
Author: Manou Liebert & Stephan Erberich
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: Modfications of spm2batch that can make a SPM user happier.
Author: Juan J. Lull Noguera
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 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: "Paxinos space" rat template based on five adult female Sprague-Dawley rats.
Author: Christian Spengere
Summary: T1-weighted MRI template based on 11 normal cynomolgus monkeys.
Author: Kevin Black
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: 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: 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: 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: 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
Summary: Three-dimensional MRI atlas of the zebra finch brain, available in Analyze format.
Author: Colline Poirier
Introduction