By members and collaborators of the Functional Imaging Laboratory

SPM Extensions


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If you notice inaccuracies or out of date links, please email the SPM manager.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 SPM12, SPM8, SPM5, SPM2, SPM99.

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

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

Quick Links


AAL | AAL2 | AAL3 | ACID | AICHA | ALI | ALVIN | AMAT | AnalyzeMovie | Anatomy | AQuA | ArtRepair | aslm | ASLtbx | at4fmri | aws4SPM | BAAD | BFAST3D | BrainNetViewer | Brainnetome | BrainSlicer | BRANT | BredeQuery | Bruker2nifti | bspmview | CAT | CCAfMRI | CLASS | Clinical | Complexity | conn | ConnExT | CPCA | DAiSS | DICOMCD_Import | Diffusion_II | DPABI | DPARSF | DRIFTER | EEGAnalyzer | EMS | ExtractVals | FASL | FAST | fECM | FDR | FieldMap | fieldmap_undistort | FieldTrip | fMRIPower | fOSA | gPPI | GraphVar | GridCAT | Grocer | HV | hMRI | IBASPM | iBrainAT | iBrainLT | IBZM_tool | ICN_Atlas | ImaGIN | INRIAlign | ISAS | lead-dbs | lesion_gnb | LI | LogTransform | MACS | Mantis | MARINA | MARS | MarsBar | MASCOI | mfBox | Masking | Masks | MEAW | MIP-C | MM | MP2RAGE | multifocal | MRTOOL | MRM | NIRS-SPM | NPBayes | NS | OCT | PETPVE12 | pTFCE | Ortho | ppi_batch_hipp | PSPM | QModeling | REST | rfxplot | RobustWLS | RS-FetMRI | rsHRF | SAfE | SAMIT | SB-Reg | SCRalyze | SDM | SGTT | SimpleROIBuilder | SnPM | SpikeDet | spm_wavelet | SPMd | SPMMouse | SSM | STEM | SUIT | SurfRend | SwE | TDT | PhysIO | TOM | TFCE | UF2C | Unwarp2 | VarTbx | VDB | Volumes | WBM | WSPM | WFU_PickAtlas | xjView | XMLTools | ASLtbx | BENtbx | SVRLSMtbx | GIFT


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

Batch Utilities:

aa | AutoSPET | BatchAAL | KULscripts | parallelize_matlabbatch | spm_segment | SPMJobs12 | spm2-batch | spm2batch | spm12Batch | spmbatch | spmjob | X_batch | zephyr


AIMN_FDG_PET | Baboon | BrainDev_Atlas | Canine | Cerebellum | CCHMC_Pediatric | Dementia_PET | IPA_SPECT | Ovine | Macaca_Fascicularis | Macaca_Fascicularis_PET | Macaca_Mulatta | Macaca_Nemestrina | Rat | sCBT | SPMtemplates | UNC_Pediatric | Zebra_Finch


AAL - Anatomical Automatic Labeling SPM12 SPM8 SPM5 SPM2 SPM99

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

Author: Gin

URL: http://www.gin.cnrs.fr/AAL

AAL2 - Anatomical Automatic Labeling 2 SPM12

Summary: Implementation of a new parcellation of the orbitofrontal cortex in the automated anatomical labeling atlas, as described in Rolls et al. NI 2015.

Author: Gin

URL: http://www.gin.cnrs.fr/AAL2

AAL3 - Anatomical Automatic Labeling 3 SPM12

Summary: New parcellations in the automated anatomical labeling atlas now include divisions of the thalamus, anterior cingulate cortex, ventral striatum, etc, as described in Rolls et al. NI 2020.

Author: Rolls, Huang, Joliot

URL: https://www.gin.cnrs.fr/en/tools/aal/

ACID - Artefact correction in diffusion MRI SPM12 SPM8

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

URL: http://www.diffusiontools.com/

AICHA - An atlas of intrinsic connectivity of homotopic areas SPM12

Summary: An atlas of intrinsic connectivity of homotopic areas, as described in Joliot et al. J Neuroscience Methods 2015.

Author: Gin

URL: http://www.gin.cnrs.fr/AICHA

ALI - Automated Lesion Identification SPM12 SPM8 SPM5

Summary: ALI 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.

Author: Mohamed Seghier

URL: Contact email above

ALVIN - Automatic Lateral Ventricle delIneatioN SPM8

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

URL: http://sites.google.com/site/mrilateralventricle/

AMAT: A meta-analysis toolbox SPM2

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

URL: http://www.antoniahamilton.com/amat.html

AnalyzeMovie - AVI movies from Analyze images SPM99

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

Author: Robert Welsh

URL: http://www.sph.umich.edu/ni-stat/AnalyzeMovie.tar

Anatomy - SPM Anatomy toolbox SPM8 SPM5 SPM2 SPM99

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: 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.

Author: Antonios Antoniou and Juan J. Lull

URL: http://www.ibime.upv.es/mi/

ArtRepair - Artifact Repair toolbox SPM12 SPM8 SPM5 SPM2

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

aslm - a slightly modified asl-module SPM8

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

URL: http://aslm.sourceforge.net


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

URL: http://www.cfn.upenn.edu/~zewang/ASLtbx.php

at4fmri - adaptive thresholding of fMRI maps SPM8

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.

Author: Chris Filo Gorgolewski and Cyril Pernet

URL: http://sourceforge.net/projects/at-4-fmri/

aws4SPM SPM12 SPM8

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

Author: Chiara D'Alonzo, Devy Hoffmann and Karsten Tabelow

URL: http://www.wias-berlin.de/software/imaging/aws4SPM.jsp

BAAD - Brain Anatomical Analysis using Diffeomorphic deformation SPM12

Summary: BAAD (Brain Anatomical Analysis using Diffeomorphic deformation) is a VBM (voxel-based Morphometry) software package based on SPM12. In this software package, we present Alzheimer's Disease Score (ADS) developed using Support Vector Machine for Alzheimer's disease research. ADS used ADNI database in North America as its training data. With this software, we also hope to streamline VBM analysis for the usability in clinical settings.

Author: Akihiko Shiino

URL: http://www.shiga-med.ac.jp/~hqbioph/BAAD(English)/BAAD.html

BFAST3D - Bayesian Fast Accurate Spatial Tricks in 3D SPM12

Summary: Extends 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).

Author: Per Siden

URL: https://github.com/psiden/BFAST3D

BrainNet Viewer

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

URL: http://www.nitrc.org/projects/bnv/

Brainnetome Atlas Viewer

Summary: 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.

Author: Congying Chu, Lingzhong Fan, Tianzi Jiang

URL: http://atlas.brainnetome.org/


Summary: BrainSlicer is a command-line image viewer. Its main purpose is to produce high-quality publication-ready figures. Main functionalities include: (1) possibility of overlaying multiple images with adjustable opacity, (2) thresholding and clusterization of each layer, (3) visualize colorbar for each desired layer, (4) handy visualization of p-value maps as (1-p), and (5) around 100 colormaps available (including FSL and brain colours maps).

Author: Daniele Mascali

URL: https://github.com/dmascali/BrainSlicer

BRANT (BRAinNetome fMRI Toolkit) SPM12 SPM8

Summary: BRANT (BRAinNetome fMRI Toolkit) is a MATLAB based toolbox which includes batch scripts with automatically generated GUIs for the preprocessing pipeline, brain spontaneous activity, functional connectivity analysis, complex network analysis, statistical analysis and results visualization. A universal input/output interface was designed for most functions, and users can customize their own scripts into GUIs by adding a few lines of MATLAB code. We've also implemented efficient file loading/saving functions and parallel computing scripts using matrix operations, OPENCL and multithreading to speed up data processing.

Author: Kaibin Xu, Yong Liu, Tianzi Jiang

URL: http://brant.brainnetome.org/en/latest/

BredeQuery SPM5

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

URL: http://neuro.imm.dtu.dk/wiki/BredeQuery

Bruker2nifti SPM12 SPM8 SPM5

Summary: Bruker raw (Paravision 6) to Nifti converter.

Author: Cristina Chavarrias

URL: https://github.com/CristinaChavarrias/Bruker2nifti

bspmview SPM12 SPM8

Summary: Another 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).

Author: Bob Spunt

URL: http://spunt.github.io/bspmview/

Computational Anatomy Toolbox SPM12

Summary: This 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.

Author: Christian Gaser and Robert Dahnke

URL: http://www.neuro.uni-jena.de/cat/


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

URL: http://cca-fmri.sourceforge.net/

CLASS - Classifier Learning for Asymmetrically Small Samples SPM8

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

Clinical Toolbox SPM12 SPM8

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: https://www.nitrc.org/projects/clinicaltbx/

Complexity SPM8

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

URL: http://loft-lab.org/index-5.html

conn - Functional Connectivity Toolbox SPM12 SPM8

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

URL: https://www.nitrc.org/projects/conn

ConnExT - Connectivity Explorer Toolbox SPM8

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

URL: https://github.com/gcbeltramini/spm-extensions/tree/master/ConnExT


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

URL: http://www.nitrc.org/projects/fmricpca


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

URL: https://github.com/SPM/DAiSS


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

URL: http://allserv.ugent.be/~pvdemael

Diffusion II - Post-processing for diffusion weighted image series SPM12 SPM8 SPM5 SPM2

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

URL: http://sourceforge.net/projects/spmtools

DPABI - Data Processing & Analysis of Brain Imaging SPM8

Summary: A toolbox for Data Processing & Analysis of Brain Imaging, evolved from DPARSF.

Author: Chao-Gan Yan

URL: http://dpabi.org/

DPARSF- Data Processing Assistant for Resting-State fMRI SPM8 SPM5

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

URL: http://rfmri.org/DPARSF

DRIFTER - An SPM toolbox for removing periodic noise in fMRI data SPM8

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

URL: https://users.aalto.fi/~asolin/documents/DRIFTER-toolbox-2012-04-25.zip

EEG Analyzer SPM12

Summary: The "EEG Analyzer" toolbox for SPM provides a user-friendly interface for M/EEG visualization. It reads SPM M/EEG files and also offers basic M/EEG filtering options. If present, events are also shown.

Author: Rudy Ercek

URL: https://bitbucket.org/ulbeeg/eeganalyzer

EMS - Expectation Maximization Segmentation SPM2

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

URL: http://www.medicalimagecomputing.com/downloads/ems.php

ExtractVals SPM2

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

Author: Robert Welsh

URL: http://www-personal.umich.edu/~rcwelsh/ExtractVals.tar

F-ASL - Arterial Spin Labeling functional MRI data SPM8 SPM5

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

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

FAST - fMRI artefact rejection and sleep scoring toolbox SPM12 SPM8

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

URL: http://www.montefiore.ulg.ac.be/~phillips/FAST.html

fECM - Fast eigenvector centrality mapping SPM12 SPM8 SPM5

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

FDR - False Discovery Rate SPM99

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

Author: Thomas Nichols

URL: http://www.nisox.org/Software/fdr/

FieldMap Toolbox SPM2

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

URL: http://www.fil.ion.ucl.ac.uk/spm/toolbox/fieldmap/

fieldmap_undistort - EPI distortion correction SPM99

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

Author: Rhodri Cusack

URL: http://imaging.mrc-cbu.cam.ac.uk/imaging/FmReference

FieldTrip SPM12 SPM8

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

URL: http://fieldtrip.fcdonders.nl/


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

URL: http://fmripower.org/


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: An 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.

Author: Donald McLaren

URL: http://www.nitrc.org/projects/gppi

GraphVar - comprehensive graph analyses of functional brain connectivity

Summary: 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.

Author: Johann Kruschwitz

URL: http://www.rfmri.org/GraphVar

GridCAT - Grid Code Analysis Toolbox SPM12

Summary: The GridCAT allows users to carry out automated analysis of human grid cell codes in fMRI data. The GridCAT performs all analyses, from estimation and fitting of the grid code in the general linear model, to the generation of grid code metrics and plots. It provides a graphical user interface for researchers less comfortable with programming; researchers confident with programming, however, can edit the open-source code accompanying the GridCAT to implement their own analysis pipelines. An example dataset is provided together with a detailed manual, so that users can explore the GridCAT's functionality.

Author: Matthias Stangl, Jonathan Shine, Thomas Wolbers

URL: http://www.nitrc.org/projects/gridcat

Grocer SPM8 SPM5

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.

Author: Senhua Zhu, Hengyi Rao and Siyuan Hu

URL: http://code.google.com/p/fmrigrocer/


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

Author: jung diagnostics GmbH

URL: https://jung-diagnostics.de/en/tools

hMRI-toolbox SPM12

Summary: The hMRI-toolbox (Tabelow et al. 2019) is an easy-to-use open-source and flexible tool, for quantitative MRI (qMRI) data handling and processing. It allows the estimation of high-quality multi-parameter qMRI maps (longitudinal and effective transverse relaxation rates R1 and R2*, proton density PD and magnetisation transfer MT saturation) (Weiskopf et al., 2013), followed by spatial registration in common space for statistical analysis (Draganski et al., 2011). The toolbox can be easily combined with existing SPM toolboxes for estimating diffusion MRI parameter maps, and it benefits from the extensive range of established SPM tools for high-accuracy spatial registration and statistical inferences. The qMRI maps generated by the toolbox can be used for quantitative parameter analysis and accurate delineation of subcortical brain structures. They are key input parameters for biophysical models designed to estimate tissue microstructure properties such as the MR g-ratio and to derive standard and novel MRI biomarkers (Mohammadi et al., 2015). The hMRI toolbox is therefore a first step towards in vivo histology using MRI (hMRI) and is being extended further in this direction.

Author: See website

URL: http://www.hmri.info/

IBASPM (Individual Brain Atlases using SPM) SPM5 SPM2

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.

Author: Lester Melie Garcia and Yasser Aleman-Gomez

URL: http://www.thomaskoenig.ch/Lester/ibaspm.htm

iBrain analysis toolbox SPM8 SPM5 SPM2

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

URL: http://brain.org.au/iBrain/#ibrain_spmtools

iBrain Laterality Toolbox SPM8 SPM5 SPM2

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

URL: http://brain.org.au/iBrain/#ibrain_li

IBZM-tool - Expert system for evaluation of IBZM SPECT studies SPM2

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

URL: ftp://ftp.uke.uni-hamburg.de/pub/nuklearmedizin/

ICN Atlas SPM12 SPM8

Summary: ICN_Atlas is an SPM8 and SPM12 compatible toolbox that is aimed at facilitating the interpretation of neuroimaging data in the context of intrinsic connectivity networks (ICNs, a.k.a. resting-state networks or RSNs) by describing fMRI activation maps or other statistical maps in function-oriented, objective and quantitative way using a set of 15 metrics conceived to quantify the degree of 'engagement' of ICNs for any given statistical map of interest. Besides the functionally-derived atlasing capabilities (based on the BrainMap ICN data) the toolbox provides anatomy-based atlasing (based on the JHU and Brainnetome Atlas data), as well.

Author: Lajos R Kozak

URL: https://www.nitrc.org/projects/icn_atlas/


Summary: SPM-based toolbox for processing intracranial EEG recordings (sEEG and ECoG), including advanced features for the analysis of epilepsy and cortico-cortical evoked potentials (CCEP).

Author: Olivier David, Viateur Tuyisenge, Lena Trebaul, Francois Tadel

URL: https://f-tract.eu/software/imagin/

INRIAlign - Motion correction with reduced paradigm-correlation bias SPM99

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

ISAS - Ictal-Interictal SPECT Analysis by SPM SPM2

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

URL: http://spect.yale.edu

lead-dbs SPM12 SPM8

Summary: A MATLAB Toolbox for DBS electrode reconstructions and visualizations based on postoperative MRI and CT imaging.

Author: Andreas Horn

URL: http://www.lead-dbs.org/

lesion_gnb Toolbox SPM12

Summary: The 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.

Author: Joseph Griffis

URL: https://www.researchgate.net/profile/Joseph_Griffis/contributions

LI-toolbox SPM12 SPM8

Summary: Allows 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.

Author: Marko Wilke

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

LogTransform SPM12 SPM8

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

URL: http://audio-fmri.langers.nl/files/logtransform.zip

MACS - Model Assessment, Comparison and Selection SPM12

Summary: This is an SPM toolbox for model assessment, comparison and selection (MACS) of general linear models (GLMs) applied to functional magnetic resonance imaging (fMRI) data. It includes classical, information-theoretic and Bayesian measures of model quality as well as implementations of cross-validated Bayesian model selection (cvBMS) and cross-validated Bayesian model averaging (cvBMA).

Author: Joram Soch

URL: https://github.com/JoramSoch/MACS

Mantis SPM12

Summary: The 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.

Author: Richard Beare

URL: http://developmentalimagingmcri.github.io/mantis/

MARINA - MAsks for Region of INterest Analysis SPM2

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

URL: http://www.bion.de/eng/MARINA.php

MARS - Morphologically and Anatomically accuRate Segmentation SPM8

Summary: MARS 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.

Author: Yu (Andy) Huang

URL: http://www.parralab.org/mars/

MarsBar - MARSeille Boite A Region d'interet SPM12 SPM8 SPM5 SPM2 SPM99

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

URL: http://marsbar.sourceforge.net/

MASCOI - Masked Contrast Images SPM5 SPM2

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/

mfBox - The model-free toolbox SPM5

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.

Author: Peter Gruber, Fabian Theis, Ingo Keck

URL: http://mfbox.sourceforge.net/

Masking Toolbox SPM8 SPM5 SPM2

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

URL: http://www.cs.ucl.ac.uk/staff/g.ridgway/masking

Masks SPM2 SPM99

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/

MMEEG Automated Workflow System (MEAW SYSTEM) SPM12

Summary: The toolbox allows us to analyse MEG data (so far only Yokogawa-KIT and Ricoh system) full automated. Statistical results are also given based on the normative database.

Author: Yoshihito Shigihara

URL: https://www.hokuto7.or.jp/hospital/lang/english-home/meaw/

MIP-C - Maximum Intensity Projection with colors SPM8

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

URL: https://github.com/gcbeltramini/spm-extensions/tree/master/MIP-C

MM - Multivariate Methods for fMRI SPM5 SPM99

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: This extension is related to MP2RAGE sequence. The first job removes the noise background of the UNI image, helping for segmentation. To determine the regularization parameter, an interactive version of the job shows the effects of the chosen parameter value in real time. The second job allows to estimate T1map and R1map, using the UNI image and sequence parameters. This extension is an implementation of https://github.com/JosePMarques/MP2RAGE-related-scripts compatible with the SPM Batch System.

Author: Benoit Beranger

URL: https://github.com/benoitberanger/mp2rage

multifocal - Create multifocal fMRI designs SPM2

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

URL: http://neuro.hut.fi/~vanni/data/Multifocal.zip

MRTOOL - Toolbox for structural MR imaging analyses SPM12

Summary: In view of the increasing availability of MR imaging data for clinical investigations, we introduce MRTool, a comprehensive collection of analysis tools in the form of a SPM12 plugin toolbox. At the current stage, it consists of four modules. (1) 'T1-w/T2-w image' for the generation of the multimodal ratio image. (2) 'Optimized Bias Correction parameters' for the definition of the optimal set of input parameters (regularization and FWHM) required during the bias correction of MR images in SPM12. (3) 'Brain Extraction' for the generation of skull-stripped images. (4) 'Optimized Normalization' for an enhanced spatial registration and segmentation of elderly subjects characterized by a marked ventricular enlargement and advanced atrophy.

Author: Marco Ganzetti

URL: http://www.nitrc.org/projects/mrtool/

MRM - Multivariate and Repeated Measures SPM12

Summary: A user-friendly MATLAB toolbox for group-level multimodal and repeated-measures models, using a multivariate GLM approach with permutation-based inference.

Author: Martyn McFarquhar & Shane McKie

URL: http://www.click2go.umip.com/i/software/mrm.html


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

URL: http://bispl.weebly.com/nirs-spm.html


Summary: User-friendly MATLAB GUI that implements a spatio-temporal nonparametric Bayesian modeling approach for the analysis of task-related fMRI data from multi-subject experiments.

Author: Erik Kook

URL: https://github.com/rimehi/NPBayes_fMRI

NS - Non-Stationary Cluster Extent Correction SPM5 SPM2

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

URL: http://fmri.wfubmc.edu/cms/software#NS

Optimized Censoring Toolbox SPM12

Summary: This toolbox aims to identify outliers in single subject first level fMRI studies. It combines three outlier indicators which are balanced by the Akaike information criteria. It is applicable to task-based as well as resting state fMRI.

Author: Marko Wilke

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

PETPVE12 - Partial Volume Effects correction of PET images SPM12

Summary: This toolbox implements two popular algorithms for partial volume correction (PVC) of PET images within an easy to use GUI-based pipeline that provides high transparency and flexibility with respect to the implemented routines, processing choices and parameter settings for the distinct PVC methods. The implemented algorithms include the "Muller-Gartner" method for 3-compartmental voxel-wise PVC, and the "Geometric Transfer Matrix/Rousset" method for region-wise PVC. Some of the toolbox routines require Matlab's Image Processing Toolbox.

Author: Gabriel Gonzalez-Escamilla & Michel Grothe

URL: https://github.com/GGonEsc/petpve12

pTFCE - probabilistic TFCE SPM12

Summary: PTFCE (probabilistic TFCE) is a cluster-enhancement method to improve detectability of neuroimaging signal. Similarly to the original TFCE approach, it performs topology-based belief boosting by integrating cluster information into voxel-wise statistical inference. However, pTFCE is more robust to various signal topologies and is significantly faster to compute, since it requires no permutation tests.

Author: Tamas Spisak

URL: https://spisakt.github.io/pTFCE/

Ortho - Visualisation and ROI analysis SPM8 SPM5

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

URL: http://www.eecs.umich.edu/~hernan/Public/Programs/

PSPM - Parallel SPM SPM2

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

Author: Jejo Koola

URL: http://prdownloads.sourceforge.net/parallelspm/

QModeling SPM12 SPM8

Summary: QModeling is a multiplatform toolbox for SPM to fit reference-region kinetic models (SRTM, SRTM2 and Patlak Reference are currently available in QModeling) to dynamic PET studies. The toolbox was developed in the bioengineering department of the Molecular Imaging Unit at CIMES (FGUMA) in collaboration with the department of Computer Science and Programming Languages at Malaga University (UMA).

Author: Molecular Imaging Unit at CIMES (FGUMA)

URL: http://www.uimcimes.es/contenidos/golink?p=1

REST - Resting-state fMRI data analysis toolkit SPM8 SPM5 SPM2 SPM99

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

URL: http://resting-fmri.sourceforge.net/

SB-Reg - Segmentation-based Multimodal Rigid Image Registration SPM12

Summary: This Matlab function extends SPM12’s spm_coreg function, allowing rigid registration of 3D multi-modal images based on simultaneous segmentation, as introduced by Aganj and Fischl (IEEE SPL 2017).

Author: Iman Aganj

URL: https://www.nitrc.org/projects/sb-reg

rfxplot - Visualisation of Group Inference Data SPM5

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

URL: http://rfxplot.sourceforge.net/

RobustWLS - Robust regression using Weighted-least-squares SPM12 SPM8 SPM5 SPM2

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.diedrichsenlab.org/imaging/robustWLS.html

RS-FetMRI: a "structural-free" preprocessing pipeline for fetal resting-state functional MRI SPM12

Summary: The Resting-State Fetal functional MRI (RS-FetMRI) preprocessing pipeline is a semi-automatic and easy-to-use standardized fetal rs-fMRI "structural-free" preprocessing pipeline completely integrated in MATLAB-SPM. RS-FetMRI is divided into 6 inter-dependent preprocessing modules (i.e. M1 to M6): M1) from the original sessions to reoriented volumes; M2) from 1st pass masking to realignment and 1st scrubbing procedure (within-session); M3) from with-in session reference volume segmentation to 2nd pass masking and creation of the mean reference volume between-session; M4) realignment and 2nd scrubbing procedure (between-session); M5) from mean between-session reference volume segmentation to spatial normalization of the mean between-session reference volume ; M6) from mean reference masking of all volumes to spatial normalization and smoothing.

Author: Nicolo Pecco & Pasquale Anthony Della Rosa

URL: https://github.com/NicoloPecco/RS-FetMRI

rsHRF - resting state HRF estimation and deconvolution SPM12

Summary: This toolbox is aimed to retrieve the onsets of pseudo-events triggering an hemodynamic response from resting state fMRI BOLD voxel-wise signal. It is based on point process theory, and fits a model to retrieve the optimal lag between the events and the HRF onset, as well as the HRF shape, using either the canonical shape with two derivatives, or a (smoothed) Finite Impulse Response. Once that the HRF has been retrieved for each voxel, it can be deconvolved from the time series (for example to improve lag-based connectivity estimates), or one can map the shape parameters everywhere in the brain (including white matter), and use the shape as a pathophysiological indicator.

Author: Guo-Rong Wu and Daniele Marinazzo

URL: https://github.com/compneuro-da/rsHRF

SAfE - Straightforward Analysis of fMRI and EEG-fMRI SPM8

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

URL: https://github.com/gcbeltramini/spm-extensions/tree/master/SAfE

SAMIT - Small Animal Molecular Imaging Toolbox SPM12 SPM8

Summary: The 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.

Author: David Vallez Garcia

URL: http://mic-umcg.github.io/samit/

SCRalyze SPM8

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

Author: Dominik R. Bach

URL: http://scralyze.sourceforge.net/

SDM - Signed Differential Mapping SPM8 SPM5

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

URL: http://www.sdmproject.com/

SGTT - Synaptic Gains Tracking Toolbox SPM12

Summary: SGTT, a SPM EEG synaptic gains tracking toolbox, allows to 1) track the average excitatory Ae, slow and fast inhibitory synaptic gains, B and G, by automatically fitting EEG data to a neural mass model; 2) compute four synaptic gain ratios (excitatory/slow inhibitory Ae/B, excitatory/fast inhibitory Ae/G, excitatory/(slow + fast) inhibitory Ae/(B+G), and slow/fast inhibitory ratio B/G, and smooth them using moving average filter; 3) display the path to epilepsy through the synaptic gain space.

Author: Xiaoya Fan, Rudy Ercek & Antoine Nonclercq

URL: https://www.researchgate.net/publication/347523446_Synaptic_Gains_Tracking_Toolbox

SimpleROIBuilder - Easy creation of simple ROIs SPM5 SPM2

Summary: Creates mask images based on spheres or boxes.

Author: Robert Welsh

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

SnPM - Statistical Nonparametric Mapping SPM12 SPM8 SPM5 SPM2 SPM99

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

URL: http://www.nisox.org/Software/SnPM

SPM EEG Spike detection toolbox SPM12

Summary: SpikeDet is a fully automated method of interictal spike detection in an EEG record that adapts to interpatient and intrapatient variation in spike morphology. The algorithm works in five steps. (1) Spikes are detected using parameters suitable for highly sensitive detection. (2) Detected spikes are separated into clusters. (3) The number of clusters is automatically adjusted. (4) Centroids are used as templates for more specific spike detections, therefore adapting to the types of spike morphology. (5) Detected spikes are summed.

Author: Antoine Nonclercq & Rudy Ercek

URL: https://www.researchgate.net/publication/321699573_SPM_EEG_Spike_detection_toolbox

spm_wavelet - Spatial wavelet denoising SPM5 SPM2

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

SPMd - Statistical Parametric Mapping Diagnosis SPM5 SPM2 SPM99

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

URL: http://www.nisox.org/Software/spmd/

SPMMouse - Animal brain toolbox SPM12 SPM8 SPM5

Summary: SPMMouse 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.

Author: Stephen Sawiak

URL: http://www.spmmouse.org/

SSM PCA - A multivariate toolbox for brain mapping analysis SPM5 SPM2 SPM99

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

URL: http://feinsteinneuroscience.org/imaging-software

STEM - Smoothing and Testing of Local Maxima SPM12

Summary: This package provides functions for computing exact peak p-values and performing FDR peak inference inference on smooth random fields. It implements the methods, comparison simulations to SPM12, and data analysis as reported in Schwartzman and Telschow (2018).

Author: Fabian Telschow and Armin Schwartzman

URL: https://github.com/ftelschow/STEM

SUIT - Spatially unbiased infra tentorial template for normalization of cerebellum and brainstem SPM12 SPM8

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

URL: http://www.diedrichsenlab.org/imaging/suit.htm

SurfRend - Surface rendering of statistic maps SPM5 SPM2 SPM99

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

Author: Itamar Kahn

URL: http://spmsurfrend.sourceforge.net/

SwE - Sandwich Estimator Toolbox for Longitudinal & Repeated Measures Data SPM12 SPM8

Summary: SwE 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).

Author: Bryan Guillaume & Thomas Nichols

URL: http://nisox.org/Software/SwE/

TDT - The decoding toolbox SPM12 SPM8 SPM5 SPM2

Summary: The 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.

Author: Martin Hebart, Kai Gorgen

URL: https://sites.google.com/site/tdtdecodingtoolbox/

TAPAS PhysIO Toolbox SPM12 SPM8

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: https://www.translationalneuromodeling.org/tapas

Template-O-Matic toolbox SPM8 SPM5

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

URL: https://irc.cchmc.org/software/tom.php

TFCE Toolbox SPM12

Summary: This toolbox offers non-parametric statistics based on threshold-free cluster enhancement (TFCE). The toolbox can be applied to (almost) any existing statistical (parametric) SPM design for 3D volume or surface data.

Author: Christian Gaser

URL: http://www.neuro.uni-jena.de/tfce/

UF2C - User Friendly Functional Connectivity SPM12 SPM8

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

URL: https://www.lniunicamp.com/uf2c

Unwarp Toolbox SPM2

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

URL: http://www.fil.ion.ucl.ac.uk/spm/toolbox/unwarp/

VarTbx - Variability Toolbox SPM12 SPM8

Summary: Measures within-voxel time series variability in fMRI data.

Author: Stefan Schmidt & Douglas Garrett

URL: http://douglasdgarrett.com/software


Summary: The software package VDB 1.0 has been designed for analysis neural activities of brain regions evoked by the virtual stimulating signal (or the virtual task signal). In addition, this tool can also help researchers to study causal relationships among brain regions. Current version of this software package is VDB1. 0. The current release is designed for the analysis of resting-sate fMRI. VDB 1.0 software package had been tested in Windows 7/Windows 10(32 and 64 bit) platforms. This software uses the 4D NIFTI-1 file format for the image data. All images must be written as 4D NIFTI-1. All data must be preprocessed by using SPM before these data can be processed utilizing the software package VDB1. 0.

Author: Guang-Yu Zhang & Hua Ma

URL: https://www.nitrc.org/projects/vdb/

Volumes Toolbox SPM12 SPM8 SPM5 SPM2

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

URL: http://sourceforge.net/projects/spmtools

Wavelet-based Morphometry SPM8 SPM5 SPM2

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 requires Linux / Unix or Mac OS.

Author: Erick J. Canales-Rodriguez

URL: http://www.wbmorphometry.com/

Wavelet-based SPM SPM8 SPM5 SPM2

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

URL: http://miplab.epfl.ch/wspm/

WFU_PickAtlas SPM12 SPM8 SPM5 SPM2 SPM99

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

URL: http://www.nitrc.org/projects/wfu_pickatlas/

xjView - Viewing tool SPM12 SPM8 SPM5 SPM2

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

URL: https://www.alivelearn.net/xjview/


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: ASLtbx 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.

Author: Ze Wang

URL: http://www.cfn.upenn.edu/~zewang/ASLtbx.php


Summary: BENtbx (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.

Author: Ze Wang

URL: http://www.cfn.upenn.edu/~zewang/BENtbx.php

SVR-LSM toolbox SPM8

Summary: SVR-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.

Author: Ze Wang

URL: http://www.cfn.upenn.edu/~zewang/software.html

GIFT - Group ICA of fMRI Toolbox SPM8

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

Author: Vince Calhoun

URL: http://mialab.mrn.org/software/



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

Author: Kayako Matsuo

URL: http://aveli.web.fc2.com/

BrainMagix SPM Viewer SPM8 SPM5

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

URL: http://www.imagilys.com/brainmagix-spm-viewer/

Bruker2Analyze - Bruker Paravision to Analyze converter SPM99

Summary: Windows program to convert Bruker to Analyze files.

Author: Chris Rorden

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

CBMG-Tools - Utilities for analysis, display, etc SPM99

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

URL: http://www.brain.northwestern.edu/cbmg/cbmg-tools/

Design Magic - Multicollinearity assessment for fMRI designs SPM2 SPM99

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

URL: http://www.matthijs-vink.com/tools.html

dicom2nifti SPM8 SPM5

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

URL: http://www.aimfeld.ch/neurotools/neurotools.html

Dynamic PET - Quantification of dynamic PET studies SPM2

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

URL: http://www.sbirc.ed.ac.uk/LCL/LCL_M1.html

Easy_Volumes SPM8 SPM5

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

Author: Cyril Pernet

URL: http://www.sbirc.ed.ac.uk/LCL/LCL_M1.html

FDRill - Plot T image histogram and FDR PP-plot SPM2

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

URL: http://www.nisox.org/files/Matlab/FDR/FDRill.m

Fluctuation - Task-independent connectivity discussion group SPM5 SPM2 SPM99

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

URL: http://www.nitrc.org/projects/fluctuations

fToolbelt - Functional Toolbelt SPM99

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/

Fractional Anisotropy Database SPM2

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

Author: Khin Khin Tha

URL: http://rad.med.hokudai.ac.jp/research/fa/

GA - Genetic Algorithm for Experimental Design SPM8 SPM5 SPM2 SPM99

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

GE2SPM - Convert data from GE to SPM Analyze SPM99

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

JG - John's Gems SPM5 SPM2 SPM99

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

URL: https://blog.nisox.org/tag/johns-gems/


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

Author: Sergey Pakhomov

URL: http://www.ihb.spb.ru/~pet_lab/L2S/L2SMain.htm

log_roi_batch - Script for ROI value extraction SPM8 SPM5

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

URL: http://www.aimfeld.ch/neurotools/neurotools.html

LMGS - Remove global effects from fMRI images SPM12 SPM8 SPM5 SPM2 SPM99

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

URL: https://github.com/paulmmacey/lmgs

MatlabTFCE - Standalone MATLAB implementation of permutation TFCE correction

Summary: 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.

Author: Mark Thornton

URL: https://github.com/markallenthornton/MatlabTFCE

Motion Fingerprint SPM12 SPM8

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/

mri_toolbox - Analyze read/write utilities SPM99

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

URL: http://eeg.sourceforge.net

MSU - MNI Space Utility SPM5 SPM2 SPM99

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

URL: http://www.ihb.spb.ru/~pet_lab/MSU/MSUMain.html

Orthviews Plugins - Reorient, Diffusion tensor visualization, and more! SPM5 SPM2

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

URL: http://sourceforge.net/projects/spmtools

Protocol for PPI connectivity analysis of all hippocampal voxels SPM12

Summary: Batch files from this site generate PPI connectivity maps from every voxel in the normalized hippocampus, including average maps computed from different sectors of the hippocampus. The downloaded zip file includes a copy of the directory structure used by the batch files, a protocol with and without annotations for detailed explanations and trouble-shooting tips, and related files necessary for executing the batch files. The approach used provides a sensitive means to examine task-specific connectivity from all regions of the hippocampus, particularly useful when the precise region of interest is unknown (see “Topography of Hippocampal Connectivity with Sensorimotor Cortex Revealed by Optimizing Smoothing Kernel and Voxel Size” at https://doi.org/10.1101/2020.05.14.096339).

Author: Douglas Burman

URL: https://www.nitrc.org/projects/ppi_batch_hipp/

PCT - Percent Change Threshold SPM99

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

Author: Thomas Nichols

URL: http://www-personal.umich.edu/~nichols/PCT/

pvconv.p - A Bruker data converter SPM99

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

Author: Matthew Brett

URL: http://pvconv.sourceforge.net/

r2agui - A Philips PAR/REC to Analyze/NifTI data converter SPM5 SPM2

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

URL: http://r2agui.sourceforge.net

SEM - Structural Equation Modelling (SEM) for fMRI SPM8 SPM5 SPM2 SPM99

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://dslink333.dyndns.org/SEM.htm

slice_overlay SPM2

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://imaging.mrc-cbu.cam.ac.uk/imaging/DisplaySlices

TSDiffAna - translates somehow into timeseries difference analysis SPM12 SPM8 SPM5 SPM2

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

URL: http://sourceforge.net/projects/spmtools

TSU - Talairach Space Utility SPM5 SPM2 SPM99

Summary: Visualization of SPM99 clusters on Talairach atlas sections.

Author: Sergey Pakhomov

URL: http://www.ihb.spb.ru/~pet_lab/TSU/TSUMain.html

iTT Toolbox SPM8 SPM5

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

Author: Tibor Auer

URL: https://github.com/tiborauer/iTT

VBMtools - Collection of scripts and hints for VBM SPM8 SPM5 SPM2

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

URL: http://dbm.neuro.uni-jena.de/vbm/

vis - SPM image visualization SPM8 SPM5

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

URL: http://tools.robjellis.net

visionToSPM - SIEMENS Vision to SPM Analyze converter SPM99

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

VoiTool - Volume of Interest Tool SPM99

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

Author: Sergey Pakhomov

URL: http://www.ihb.spb.ru/~pet_lab/VTO/VTOMain.html

Batch Utilities

aa - Automatic Analysis SPM8 SPM5

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

URL: https://github.com/rhodricusack/automaticanalysis/wiki


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.

URL: http://www.autospet.altervista.org/

Batch AAL SPM8

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

KUL - KULeuven functions to automate SPM (fMRI) SPM99

Summary: Automate fMRI data post processing.

Author: Stefan Sunaert & Erik Beatse

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

parallelize_matlabbatch SPM8

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

URL: http://algoholic.eu/parallelize_matlabbatch/

spm_segment SPM5 SPM2 SPM99

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

URL: http://www.nmrgroup.ion.ucl.ac.uk/atrophy/index.html

SPMJobs12 SPM12

Summary: Batch 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.

Author: Jerry Zhu

URL: http://zhupsy.com/more

spm2-batch SPM2

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

URL: http://spm2-batch.sourceforge.net/

spm2batch SPM2

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

Author: Jejo Koola

URL: http://prdownloads.sourceforge.net/spm2batch/

spm12Batch SPM12

Summary: A bash-based ecosystem for doing pre-processing of fMRI data in a flexible, and reproducible manner.

Author: Robert Welsh

URL: https://github.com/rcwelsh/spm12Batch

spmbatch SPM8 SPM5

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

URL: http://www.aimfeld.ch/neurotools/neurotools.html

spmjob SPM2

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

URL: http://sourceforge.net/projects/spmjob/

X_batch SPM2

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

Author: Xenia Hertzenberg

URL: http://x-batch.sourceforge.net

Zephyr SPM2

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

Author: Craig Bennett

URL: http://prefrontal.org/wiki/index.php/Zephyr


[18F]FDG-PET brain healthy control (HC) dataset SPM12 SPM8 SPM5 SPM2 SPM99

Summary: An appropriate [18F]FDG PET brain healthy control (HC) dataset is mandatory to achieve good performance in voxel-wise image analyses, particularly on a single subject basis. Here is provided a [18F]FDG PET brain dataset of HC based on data collected by the Italian association of nuclear medicine, for the extraction of voxel-based brain metabolism maps. The performance of this HC dataset was tested in comparison with other standard reference HC datasets (see Camini, Sala, Presotto et al, EJNMMI 2021). The applied procedures ensure validity of this HC dataset for the estimation of brain metabolism at group and single-subject level, ready-to-use in research and clinical settings.

Author: Perani Daniela, Presotto Luca, Caminiti Silvia, Sestini Stelvio and the Associazione Italiana Medicina Nucleare (AIMN), the Neurology Study-Group

URL: https://aimn.it/brain-fdg/

B2K template images for neuroimaging in baboon SPM99

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

URL: http://purl.org/net/kbmd/b2k

Brain Atlases of 2-year-olds

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

Author: Daniel Rueckert

URL: http://www.brain-development.org/

Canine Brain Atlas

Summary: T2w datasets were acquired from 16 neurologically inconspicuous dogs of different breeds by 3T MRI. The datasets were averaged after initial preprocessing using linear and nonlinear registration algorithms as implemented in SPM8. TPM for gray (GM) and white matter (WM) as well as cerebrospinal fluid (CSF, and ventricles) were created. Different cortical, subcortical, medullary, and CSF regions were manually labeled to create a spatial binary atlas being aligned with the template. Overall, 21 brain regions were labeled using the segmented tissue classes of the brain template.

Author: Bjorn Nitzsche

URL: http://animal-brain-mapping.com/dog

Probabilistic atlas of the human cerebellum

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.diedrichsenlab.org/imaging/propatlas.htm

CCHMC Pediatric Atlas SPM2 SPM99

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

URL: http://www.irc.cchmc.org/software/pedbrain.php

Dementia-Specific [18F]-FDG-PET template for SPM normalization SPM12 SPM8 SPM5 SPM2 SPM99

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).

Author: Pasquale Anthony Della Rosa & Daniela Perani

URL: https://github.com/PasqualeDellaRosa/Dementia-Specific-18F-FDG-PET-template


Summary: p-[(123)I]iodo-L-phenylalanine( IPA)-SPECT template in MNI-coordinates obtained from 12 human subjects.

Author: Emilia Iannilli

URL: https://www.nitrc.org/projects/ipa-spect_templ/

Ovine Brain Atlas

Summary: 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.

Author: Bjorn Nitzsche

URL: https://www.mcgill.ca/bic/resources/brain-atlases/ovine-brain-atlas

Template images for neuroimaging in Macaca fascicularis SPM99

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

Author: Kevin Black

URL: http://purl.org/net/kbmd/cyno

MRI template of Macaca Fascicularis Brain

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

112RM-SL template images for neuroimaging in rhesus macaque (Macaca mulatta) SPM8 SPM5

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

URL: http://brainmap.wisc.edu/monkey.html

N2K template images for neuroimaging in Macaca nemestrina SPM99

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

URL: http://purl.org/net/kbmd/n2k

Karolinska Rat Atlas SPM99

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

Author: Christian Spengere

URL: http://expmr.ki.se/research/ratatlas.jsp

Statistical Chinese Brain Atlas (Chinese2020) SPM12 SPM8 SPM5 SPM2 SPM99

Summary: A statistical Chinese brain atlas based on a multi-center T1-weighted magnetic resonance imaging (MRI) dataset of 2020 Chinese adults (18-76 years old). New Chinese brain standard space, coordinates, and brain area labels were further defined.

Author: Peipeng Liang, Lin Shi, Defeng Wang & Kuncheng Li

URL: http://www.chinese-brain-atlases.org/index_en.asp

18F-DOPA and 123I-FP-CIT human templates for SPM normalisation SPM8 SPM5

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.

Author: Garcia-Gomez F.J., Garcia-Solis D.

URL: http://www.nitrc.org/projects/spmtemplates

UNC 0-1-2 Infant Atlases

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

URL: http://www.nitrc.org/projects/pediatricatlas

Zebra Finch MRI Atlas SPM2 SPM99

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/