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The literature presents (exceedingly) many methods for analysis of neuroscience data. Table 10 lists only few for use within functional and molecular neuroimaging.
| Domain | Name/topic | Description | Reference |
| Dynamic PET | ``Logan plot'', the classic Logan plot | [Logan et al., 1996] | |
| Dynamic PET | Logan's Reference Tissue Model | Logan's plot with a reference region used with 
Implemented in PMOD. |
http://pmod.com/technologies/doc/pkin/2322.htm |
| Dynamic PET | MRTM0 | Ichise's (original) multi-linear reference tissue model | [Ichise et al., 1996], http://www.pmod.com/technologies/doc/pxmod/3250.htm |
| Dynamic PET | MRTM | Ichise's (modified) multi-linear reference tissue model, a three-parameter model | [Ichise et al., 2003,Ichise et al., 2002], http://www.pmod.com/technologies/doc/pkin/2316.htm |
| Dynamic PET | MRTM2 | Ichise's multi-linear reference tissue model, a two-parameter
model with fixed |
[Ichise et al., 2003], http://www.pmod.com/technologies/doc/pxmod/3251.htm |
| fMRI BOLD response modeling | Convolution with FIR-filter | Linear modeling of the response from paradigm to fMRI signal with a finite impulse response (FIR) filter. | [Nielsen et al., 1997,Goutte et al., 2000,Lange et al., 1999] |
| fMRI response modeling | Convolution with Bayesian estimated FIR | Modeling the fMRI response with a finite impulse response (FIR) filter, Bayesian estimation, a Gaussian process prior, and Markov chain Monte Carlo (MCMC) | [Goutte et al., 2000,Andersen et al., 2002], |
| fMRI BOLD response modeling | Convolution, Gamma | A gamma probability density function modeling the hemodynamic response, estimation in the frequency domain, and modeling of the noise in the frequency domain. Partly implemented in Lyngby | [Lange and Zeger, 1997] |
| fMRI BOLD response modeling | Bayesian balloons | Balloon models, extended balloon models with Bayesian Markov chain Monte Carlo and split-half resampling. | [Jacobsen et al., 2008] |
| fMRI unsupervised multivariate | K-means clustering | K-means clustering of voxels with use of cross-correlation function between paradigm and fMRI signal. Estimation of the number of clusters. | [Goutte et al., 1999b] |
| fMRI unsupervized multivariate | K-means clustering | Clustering of voxel based on features from, e.g., and FIR-filter modeling of the hemodynamic response | [Goutte et al., 2001,Goutte et al., 1999a] |
| fMRI unsupervised multivariate | Independent component analysis (ICA) | There are many studies in this domain | See Bibliography on Independent Component Analysis in Functional Neuroimaging |
| fMRI semi-supervized | Univariate correlation across subjects | Showing the same stimulus to several subjects and analysis the intersubject correlation, interparticipant correlation (IPC) | [Hasson et al., 2004,Hejnar et al., 2007] |
| Analysis | Image-based covariates | (Biological parametric mapping) | [Casanova et al., 2007,Oakes et al., 2007,Mehta et al., 2006] |
| Prediction | PCA and neural network classifier | Principal component analysis and an artificial neural network | [Lautrup et al., 1995,Hansen et al., 1994] |
| Prediction | Neural network classifier | SPECT predicting Alzheimer and controls | [Halkjær et al., 1997a,Halkjær et al., 1997b] |
| Prediction | PET and fMRI, neural network, principal component analysis | [Mørch et al., 1997,Mørch et al., 1995,Mørch et al., 1996] | |
| Prediction | fMRI, neural network and principal component analysis with saliency maps | [Nielsen, 1996] | |
| Prediction and reproducibility | Learning curves | Demonstrated on four different PET data sets. Prediction error expressed in terms of mutual information and sensitivity map shown. | [Kjems et al., 2002] |
| Prediction | fMRI, evolutionary algorithm feature selection, linear classifier, neural network, support vector machine with relevance maps | Prediction | [Åberg et al., 2006] |
| Connectivity modeling | Structural equation modeling, etc. | See the Bibliography on Path Analysis | |
| Imaging | Location identification | [Reimold et al., 2005] | |
| Multiple comparisons | Permutation test on the maximum in the statistical summery image | [Holmes et al., 1996,Nichols and Holmes, 2001] | |
| Multiple comparisons | False discovery rate (FDR) | Introduction of FDR into neuroimaging | [Genovese et al., 2002] |
| Multiple comparisons | Two-step FDR | [Jiang and Doerge, 2006] |
There exists a large number of programs for processing and analysis of brain signals, particularly within the functional neuroimaging field.
A review of some of the programs for fMRI analysis is available in [Gold et al., 1998]: AFNI 2.01, SPM96, Stimulate 5.0, MEDIMAX 2.01, and FIT were tested; FIASCO, Yale, and MEDx 2.0. FIT (functional imaging toolkit) does not seem to be available any longer. More recent comments on tools for fMRI appear in [Nielsen et al., 2006].
For lists of image registration software see the Image Registration bibliography: http://www.imm.dtu.dk/~fn/bib/Nielsen2001BibImage/. And for lists of brain segmentation software see the ``Bibliography of Segmentation in Neuroimaging'' http://www.imm.dtu.dk/~fn/bib/Nielsen2001BibSegmentation/.
Most programs work with volumes. The programs that allow for analysis or visualization of the 2D cortical surface are BrainVoyager, CirclePack, FreeSurfer, SureFit/Caret, SUMA, SurfRelax and McGray
Apart from the listed programs there is also, e.g., CliniViewer, a program for display of multiple MRIs [Uttecht and Thulborn, 2002].
| Name | Impl. | Description | Reference |
| 3D slicer | Visualization, segmentation, registration | [Gering et al., 1999,Gering, 1999] http://www.slicer.org/ | |
| 3DVIEWNIX | X | Commercial program for preprocessing, visualization and analysis of 3D imaging data. From the Medical Image Processing Group and University of Pennsylvania. | http://www.mipg.upenn.edu/~Vnews/ |
| ABLe | Solaris, Linux, SGI IRIX | Commercial program part of MEDx for ``Analysis of Brain Lesions'' | http://medx.sensor.com/products/medx/able.html |
| Activ2000 | Delphi5 | Windows-based program for fMRI processing and analysis. | http://www.multimania.com/dducreux/activ2000.htm |
| AFNI | C | Functional neuroimaging analysis program | [Cox, 1996,Cox and Hyde, 1997,Cox and Ward, 1997,Ward and Cox, 1997], http://afni.nimh.nih.gov/afni/ |
| AIR | C | Image registration program | [Woods et al., 1998a,Woods et al., 1998b] http://bishopw.loni.ucla.edu/AIR3/ |
| AMIDE | Unix, Mac, Windows | Volume viewing | [Loening and Gambhir, 2003], http://amide.sourceforge.net/ |
| Anatomist | Unix | Structural morphometry analysis, e.g., sulci identification. Part of BrainVISA | [Riviére et al., 2003], http://anatomist.info |
| Atamai | Linux, Mac OS X, windows | ``Atamai Viewer'' with 3D visualization. Image registration (commericial) | http://www.atamai.com/ |
| BAMM | ``[S]oftware library for statistical analysis of structural and functional magnetic resonance (MR) images'' | http://www-bmu.psychiatry.cam.ac.uk/BAMM/ | |
| BET | Brain Extraction Tool by Stephen Smith et al. Included in MRIcro | http://www.fmrib.ox.ac.uk/fsl/bet/ | |
| BPM | Matlab | ``Biological Parametric Mapping Toolbox'' matlab toolbox with image-based regressors | [Casanova et al., 2007], http://www.fmri.wfubmc.edu |
| BrainMapTM | Internet, Java | Database with functional neuroimaging results | [Fox and Lancaster, 1994,Fox et al., 1994,Fox et al., 1995,Lancaster et al., 1994,Lancaster et al., 1997a,Fox and Lancaster, 2002,Fox et al., 2005a] http://www.brainmap.org |
| BRAINS2 | X11, OpenGL, TCL/TK | ``Brain Research: Analysis of Images Networks and Systems''. Manual and automated tools for structural analysis, tissue classification and cortical surface extraction. | [Magnotta et al., 2002,Magnotta and Andreasen, 2001], http://moniz.psychiatry.uiowa.edu/local/brains2/brains2.html |
| Brain Tools | Software by Krish Singh for the Analysis of Structural and Functional Brain images. Consists of mri3dX and mriWorkshopX. | http://www-users.aston.ac.uk/~singhkd/software.html | |
| BrainVoyager | C++/OpenGL/Qt | Commercial program for fMRI analysis and visualization | http://www.brainvoyager.de/ |
| BrainWeb | Internet service | Database with simulated MRI of the human brain | [Cocosco et al., 1997,Kwan et al., 1996,Kwan et al., 1999,Collins et al., 1998] http://www.bic.mni.mcgill.ca/brainweb/ |
| BRIAN | C, C++, Unix | Perhaps continued as LIPSIA? | [Kruggel and Lohmann, 1996] |
| BSE | Automated Brain Surface Extraction | http://www.loni.ucla.edu/NCRR/Software/BSE.html | |
| CamBA | Windows, POSIX | Cambridge Brain Activation. fMRI analysis. | [Suckling et al., 2006b,Bullmore et al., 1999,Bullmore et al., 2001,Suckling and Bullmore, 2004,Suckling et al., 2006a], http://www-bmu.psychiatry.cam.ac.uk/software/ |
| Caret | SGI/Linux/Sun/Mac | `Computerized Anatomical Reconstruction and Editing Toolkit' from Van Essen Laboratory. for `visualizing, editing, analyzing, and flattening cortical surface reconstructions'. | [Drury et al., 1996,Van Essen et al., 2001,Harwell et al., 2001], http://brainmap.wustl.edu/caret/ |
| CCHIPS© | IDL | ``Cincinnati Children's Hospital Image Processing Software'' Preprocessing and analysis software for fMRI, dMRI, spectroscopy, and pMRI. | http://www.irc.chmcc.org/chips.htm |
| CirclePack | X-windows | Software for flatmapping | http://www.math.utk.edu/~kens/, http://neurovia.umn.edu/incweb/flatmap_info.html |
| CLEAVE | C | ``C Language Exploratory Analysis of Variance with Enhancements'' that is ``designed for the analysis of very large data sets of the sort obtained in experiments using EEG and fMRI'' | http://www.ebire.org/hcnlab/software/cleave.html |
| Corner Cube | IDL or Web | Visualization environment | [Rehm et al., 1998,Schaper et al., 1996,Rehm et al., 1997], http://www.neurovia.umn.edu/incweb/ccinfo.html Web demo: http://neurovia.umn.edu/incweb/ccweb/ |
| DP Tools | Delphi5 | Windows-based diffusion and perfusion MRI analysis program by Denis Ducreux | [Smith et al., 2000,Ducreux et al., 2001] http://www.multimania.com/dducreux/DPTools.htm |
| Display | Unix, OpenGL | A program to view MINC files | ftp://ftp.bic.mni.mcgill.ca/pub/register+Display/, http://www.bic.mni.mcgill.ca/software/Display/Display.html, http://sourceforge.net/projects/mni-minc-win32/ |
| EMMA | Matlab | ``Extensible MATLAB Medical image Analysis'' from BIC, MNI, McGill Reading and writing of MINC files. Visualization, ROI and dynamic PET analyses | http://www.bic.mni.mcgill.ca/software/emma/ |
| EvIdent | (Fuzzy) cluster analysis for neuroimaging | [Pizzi et al., 2001], http://www.ibd.nrc-cnrc.gc.ca/english/info_e_evident.htm | |
| FIASCO | Shell, C | Collection of programs (C and shell scripts) for processing of fMRI. | http://lib.stat.cmu.edu/~fiasco/ [Eddy et al., 1996] |
| fMRI Analysis Package (Yale) | Matlab | Analysis | http://mri.med.yale.edu/individual/pawel/fMRIpackage.html |
| FMRISTAT | Matlab | fMRI analysis program. Also called BICstat and multistat | [Worsley et al., 2002,Worsley et al., 2000] http://www.bic.mni.mcgill.ca/~keith/ |
| FMRLAB | Matlab | Independent component analysis for fMRI | http://sccn.ucsd.edu/fmrlab/ |
| FreeSurfer | Linux, Darwin, Solaris, IRIX | Program for reconstruction of the cortical surface. | [Dale et al., 1999,Fischl et al., 1999a,Fischl et al., 1999b,Fischl and Dale, 2000,Fischl et al., 2001,Busa, 2002] http://surfer.nmr.mgh.harvard.edu/ |
| FSL | C | Preprocessing and analysis in structural and functional neuroimaging by Stephen Smith et al. | [Smith et al., 2001,Smith et al., 2004], http://www.fmrib.ox.ac.uk/fsl/index.html |
| GIFT | Matlab | Group ICA of fMRI Toolbox | http://icatb.sourceforge.net/ |
| GpetView | C, Gtk+ | Simple neuroimaging visualization of ANALYZE files | http://homepage2.nifty.com/peco/gpetview/gpetview.html, Hiroshi Watabe |
| HAMMER (*) | ``Hierarchical Attribute Matching Mechanism for Elastic Registration''. Skull-stripping and elastic warping | [Shen and Davatzikos, 2002,Shen and Davatzikos, 2003], http://www.rad.upenn.edu/sbia/rsoftware.html | |
| iBrain | [Abbott and Jackson, 2001] | ||
| LIMA | C++/OpenGL | Software package for segmentation and visualization of MRIs. | [Busch et al., 2001] |
| Lipsia | C | fMRI analysis program | [Lohmann et al., 2001b,Lohmann et al., 2001a,Lohmann et al., 2000] |
| LOFA | [Gokcay et al., 1999] | ||
| Lyngby | Matlab | Neuroimaging analysis (fMRI and PET) with a number of multivariate (and univariate) analysis tools | [Hansen et al., 1999,Hansen et al., 2000,Hansen et al., 2001] http://hendrix.imm.dtu.dk/software/lyngby/ |
| MARINA | Windows, Linux with Wine | ``MAsks for Region of INterest Analysis'' enables to ``create, smooth, threshold, edit, and save masks in an SPM-ANALYZE format'' | [Walter et al., 2003], http://www.bion.de/Marina.htm |
| Martinez Flat-Mapper | Web | Flatmap and orthogonal plane visualizations of, e.g., specified Talairach coordinates | [Kang et al., 2004], http://www.ebire.org/hcnlab/cortical-mapping/ |
| MEDx | Solaris, Linux, IRIX, Tru64 | Commercial multimodality brain imaging processing and analysis software by Sensor Systems. MEDx 3.4 contains, e.g., SPM99, FSL, ABLe and ``Functional Data Simulator''. | http://medx.sensor.com/ |
| MIDAS (Tsui) | Solaris | ``Multimodal Image Data Analysis System''. Region-of interest analysis for multimodal 3D data | [Tsui et al., 2001] |
| MINC | Unix, Windows | Tools for processing MINC files | http://sourceforge.net/projects/mni-minc-win32/, http://www.bic.mni.mcgill.ca/~rotor/distro/deb/ |
| MIPAV | Java | Medical Image Processing, Analysis, and Visualization. Extensions are available for more specific neuroimaging applications. | http://mipav.cit.nih.gov/, [Bazin et al., 2007] |
| MPITool | Unix | ``Multi Purpose Imaging Tool'' from Advanced Tomo Vision. Reading and displaying of ECAT files. Reslicing, region of interest, filter. | http://www.atv-gmbh.de/mpitoolh/, [Advanced Tomo Vision, 1999] |
| MRIcro | Windows, Linux, Solaris | A program for conversion and viewing of 3D medical images by Chris Rorden. Features also region of interest (ROI) drawing and volume rendering | [Rorden and Brett, 2000], http://www.psychology.nottingham.ac.uk/staff/cr1/mricro.html |
| MRIcron | Linux, OSX and Windows (via GTK) | A program somewhat similar to MRIcro | http://www.sph.sc.edu/comd/rorden/mricron/ |
| mri3dX | Unix/OpenGL | Program by Krish Singh ``for visualization and analysis of structural and functional magnetic resonance images''. Part of Brain Tools | http://www-users.aston.ac.uk/~singhkd/mri3dX/ |
| MRIVIEW | IDL | Visualization and segmentation of 2D and 3D brain images | [Ranken and George, 1997], http://www.biophysics.lanl.gov/brain_imaging/mriview/mriview.html |
| MRIWarp | C | Image registration program for MRI | [Kjems et al., 1999b,Kjems et al., 1999a], http://hendrix.imm.dtu.dk/software/mriwarp/ |
| MRVision | Unix/Linux | Commercial program for visualization and simple fMRI analysis | http://www.mrvision.com/ |
| N3 | Correction of intensity non-uniformity in MRI | [Sled et al., 1998,Sled et al., 1997,Sled, 1997] http://www.bic.mni.mcgill.ca/software/N3/ | |
| NeuroModeller | Windows | 3D Visualization, 3D model generation from contours | http://users.infohouse.com/amiller/ |
| NIPY | Python | Neuroimaging tools for Python | http://neuroimaging.scipy.org/ |
| NPAIRS | Unix, IDL | ``Nonparametric, Prediction, Activation, Influence, Reproducibility, re-Sampling''. Package with resampling for comparing preprocessing and analysis choices and returning reproducibility and prediction indices. | [Strother et al., 2002], http://www.neurovia.umn.edu/incweb/npairs_info.html |
| PI-WAVE | Matlab | Wavelet modeling for positron emission tomography | [Turkheimer et al., 1999,Turkheimer et al., 2000a,Turkheimer et al., 2000b], http://www.irsl.org/~fet/piwave/piwave.html |
| PLS toolbox | http://www.rotman-baycrest.on.ca:8080/index.html | ||
| PMOD | Java | Kinetic modeling, viewing | [Mikolajczyk et al., 1998], http://www.pmod.com/, |
| RPM | [Aston et al., 2001] | ||
| RView8 | Windows/Unix | General purpose multimodality image registration program with display and ROI-drawing facilities | http://noodle.med.yale.edu/~cs/software/software.html |
| scanSTAT | Mac | Conversion, analysis of fMRI | http://www.brainmapping.org/scanSTAT/ |
| SPAMALIZE | IDL | ``Spect, Pet, And Mri analysis'' by Terry Oakes includes ROI drawing and analysis, interactive volume display coregistration and dynamic PET tools. | http://tezpur.keck.waisman.wisc.edu/~oakes/spam/spam_frames.htm |
| SPM | Matlab, (C mex) | Functional neuroimaging analysis program includes slice time correction, image realignment (motion, coregistration, spatial normalization), spatial filtering, analysis with the general linear model and random field theory. SPM2 features dynamic causal modeling and false discovery rate inference. | [Friston et al., 1995,Frackowiak et al., 1997,Frackowiak et al., 2003,Pernet, 2005], http://www.fil.ion.ucl.ac.uk/spm/. |
| Stimulate | C, X | Analysis and display program for fMRI | http://www.cmrr.umn.edu/stimulate/, [Strupp, 1996] |
| SUMA | Motif, OpenGL | ``SUrface MApping with AFNI''. Program for cortical-based analysis and visualization. | See AFNI |
| SuMS | ? | `Surface Management System' from Van Essen Laboratory. A software system for storing and accessing surface based data. | [Dickson et al., 2001,Van Essen et al., 2001,Harwell et al., 2001] http://stp.wustl.edu/resources/sumsnew.html |
| SureFit | Python, C | `Surface Reconstruction by Filters and Intensity Transformations' from Van Essen Laboratory. A program for segmentation, surface reconstruction and visualization of the cerebral cortex. | [Van Essen et al., 2001,Harwell et al., 2001,Van Essen et al., 2002], http://stp.wustl.edu/ |
| Talairach Daemon | Internet, Java | Talairach coordinate to anatomical label tool | [Lancaster et al., 1997b,Lancaster et al., 1997c,Freitas et al., 1996,Lancaster et al., 2000b,Lancaster et al., 2000a], http://ric.uthscsa.edu/TDapplet/, http://ric.uthscsa.edu/resources/body.html |
| Tina | xview | http://www.niac.man.ac.uk/Tina/ | |
| TSU | `Talairach Space utility'. Matlab SPM plugin | Neuroimaging visualization | http://www.ihb.spb.ru/~pet_lab/TSU/TSUMain.html |
| UCLA BMD | fMRI analysis programs containing CC_gr, T_gr, Cproto, Overlay | http://porkpie.loni.ucla.edu/BMD_HTML/SharedCode/SharedSoftware.html | |
| VINCI | Volume Imaging in Neurological Research, Co-Registration and ROIs Included | http://www.nf.mpg.de/vinci/ | |
| VoxBo | UNIX | `Software package for processing voxel-based functional brain imaging data' made at the University of Pennsylvania | http://www.voxbo.org |
| WFU PickAtlas | ROI-based analysis based on the Talairach Daemon and SPM | [Maldjian et al., 2003,Maldjian et al., 2004], http://www.fmri.wfubmc.edu/download.htm | |
| (X)MedCon | C, Gtk+ | Simple neuroimaging visualization and conversion | http://xmedcon.sourceforge.net, Erik Nolf |
|
Table 12 lists a number of execution environments (or wrappers or pipelines) which can encapsulate other programs. An execution environment typically offers a graphical user interface where program variables can be setup and the programs can be executed in arbitrary order. They will typically also allow for the storage of the parameters or the script so the setup and execution can be separated.
A few programs, e.g., SPM and AFNI, offer the possibility of plugins. SPM plugins are listed in table 13. These plugins are usually written by researchers that are not (directly) associated with the SPM developers. Note that some of the plugins are now outdated since their functionality is directly implemented in the standard distribution of later version of SPM, i.e., SPM2 and SPM5..
| Name | Description | Reference |
| ArtRepair | fMRI artifact detection and repairing by Paul Mazaika | http://cibsr.stanford.edu/tools/ArtRepair.htm |
| autospm2 | Batch scripts for SPM2 | http://www.md.ucl.ac.be/rdgn/autospm2.html |
| batch_general | Front end to SPM batch analysis by Russ Poldrack | http://sourceforge.net/projects/spm-toolbox |
| batch_subject | Toolbox by Russ Poldrack | http://sourceforge.net/projects/spm-toolbox |
| CBMG-Tools | A few function for visualization and extraction of fMRI time series | http://www.brain.northwestern.edu/cbmg/cbmg-tools/ |
| CCA-fMRI | Canonical correlation analysis for fMRI | [Borga, 1998,Friman et al., 2003], http://cca-fmri.sourceforge.net |
| Conjunction | SPM2 (1spm2_conj) and SPM99 (spm99_conj) modifications for ``conjunction null'' conjunction inference | [Brett et al., 2004], http://www.sph.umich.edu/~nichols/Conj/ |
| Deformations | Toolbox by John Ashburner with spatial normalization utilities, e.g., extraction of information from SPM99 spatial normalization file (_sn3d.mat) for deformation-based morphometry (DBM) or tensor-based morphometry (TBM) | ftp://ftp.fil.ion.ucl.ac.uk/spm/toolbox/Deformations/ |
| diffusion | Toolbox by Russ Poldrack | http://sourceforge.net/projects/spm-toolbox |
| Diffusion | Toolbox by Volkmar Glauche for diffusion weighted MRI | http://www.uke.uni-hamburg.de/kliniken/neurologie/spm/downloads/ |
| DISTANCE | Specialized permutation test. | [Mériaux et al., 2006a,Mériaux et al., 2006b], http://www.madic.org/download/DISTTBx/DISTTBx_main.html |
| Dynamic PET | Toolbox by Florian Wilke and Ralph Buchert from Hamburg includes realignment, spatial normalization, modeling of dynamic PET and SPECT and VOI analysis. | Available via email (SPM mailing list, 2000-04-04) |
| ezSPM2 | GUI for batch construction in SPM2 | http://www.izkf.rwth-aachen.de/downloads/ezspm2.htm |
| FDR | False discovery rate extension and patch for SPM by Thomas Nichols. This plugin has been included in SPM2. | http://www.sph.umich.edu/~nichols/FDR/ |
| IBASPM | ``Individual Brain Atlases using Statistical Parametric Mapping software''. SPM2 plugin that combines the AAL atlas and tissue segmentation for construction of segmentation of individuals. | http://www.thomaskoenig.ch/Lester/ibaspm.htm |
| KUL | Also called KUL_SPM, kulSPM and KULeuven. Batch script for SPM99 | http://www.kuleuven.ac.be/radiology/Research/fMRI/kulSPM/ |
| LI-Tool | SPM2/5 toolbox for computation of lateralization indices | Marko Wilke, Tübingen |
| LOR2SPM | Converts output from LORETA into SPM compatible format. Program by Sergey Pakhomov. | http://www.ihb.spb.ru/~pet_lab/L2S/L2SMain.htm |
| MarsBar | Region of interest toolbox by Matthew Brett | [Brett et al., 2002], http://www.mrc-cbu.cam.ac.uk/Imaging/marsbar.html |
| mascoi | ``MASked COntrast Images''.
A toolbox/function to combine a contrast image with  -score image |
[Reimold et al., 2005], http://homepages.uni-tuebingen.de/matthias.reimold/mci/mascoi.m |
| mfBox | Model-free toolbox | http://mips.gsf.de/proj/cmb/researchmfbox.html |
| MM Toolbox | Multivariate analysis (principal component analysis and multivariate linear models, partial least squares) by CEA-SHFJ | http://www.madic.org/download/MMTBx/ |
| MNI Space utility | Anatomical label tool | http://www.ihb.spb.ru/~pet_lab/MSU/MSUMain.html |
| PCT | `Percent Change Threshold' toolbox by Thomas Nichols | http://www.sph.umich.edu/fni-stat/PCT/ [Nichols, 2002] |
| PSPM | Parallel implementation of SPM image processing and analysis procedures using LAM/MPI and MPICH | http://sourceforge.net/projects/parallelspm/ |
| RobustWLS | A toolbox that performs weighted least squares estimation to account for artifacts, e.g., head motion. | [Diedrichsen and Shadmehr, 2005], http://www.bangor.ac.uk/~pss412/imaging/robustWLS.html |
| roi | Definition of ROI and extraction of signal by Russ Poldrack | http://sourceforge.net/projects/spm-toolbox |
| SEM | Structural equation modeling by Christian Büchel | In beta test. |
| slice_overlay | 2D visualization by Matthew Brett capable of merging an anatomical and functional image. Also called ``Slice display'' | http://www.mrc-cbu.cam.ac.uk/Imaging/display_slices.html |
| SLT | Region of interest analysis, batch scripting, semiautomated ROI identification, Contains RAT2, ASAP, SurfTools, FSTools. | [Nieto-Castanon et al., 2003,SpeechLab, 2003], http://speechlab.bu.edu/SLT.php |
| SnPM | Nonparametric permutation tests. SnPM99 is for SPM99 and SnPM2 is for SPM2 | [Nichols and Holmes, 2001,Holmes et al., 1996,Holmes, 1998], http://www.fil.ion.ucl.ac.uk/spm/snpm |
| spm2_batch (Ashburner) | Batch program for SPM2 programmed by John Ashburner | ftp://ftp.fil.ion.ucl.ac.uk/spm/toolbox/spm2_batch_031210.tar.gz (preview version) |
| spm2_batch | Batch program from SPM programmed in Cambridge | ftp://ftp.mrc-cbu.cam.ac.uk/pub/imaging/SPM2_batch |
| SPM Anatomy toolbox | Region of interest tools with probabilistic Brodmann areas atlas | [Eickhoff et al., 2005,Eickhoff, 2005], http://www.fz-juelich.de/ime/spm_anatomy_toolbox |
| spm_batch | Batch preprocessing by Sebastian Thees | http://www.charite.de/ch/neuro/forschung/teams/klinisch/people/thees/index.html |
| SPMd | `Statistical Parametric Mapping Diagnosis' by Wen-Lin Luo and Thomas Nichols for residual analysis | [Luo and Nichols, 2003], http://www.sph.umich.edu/~nichols/SPMd/ |
| spmjob | Batch processing toolbox for SPM2 with GUI. | http://spmjob.ffii.org/ |
| spm_loop | Batch processing for display multiple result images (SPMs). | http://www.mrc-cbu.cam.ac.uk/Imaging/Common/spm_loop.shtml |
| spm_orthoviews | ROI and movie tools by Volkmar Glauche. | http://www.uke.uni-hamburg.de/kliniken/neurologie/spm/downloads/ |
| SPM_Script | Front-end tool for automatic fMRI analysis | http://www.nfil.rwth-aachen.de |
| spm_xbrain | Visualization extension by Tom Sieger | http://www.neuro.lf1.cuni.cz/spm/spm_xbrain_3d.html |
| SPM XML Toolbox | A toolbox for storing point activation from SPM in the XML file format. | [Keator et al., 2005,Keator, 2005], http://www.nbirn.net/Resources/Users/Applications/xcede/SPM_XMLTools.htm |
| Talairach Space utility | Neuroimaging visualization | http://www.ihb.spb.ru/~pet_lab/TSU/TSUMain.html |
| Volumes | Toolbox by Volkmar Glauche for volume operations, e.g., extraction of subvolumes. | http://www.uke.uni-hamburg.de/kliniken/neurologie/spm/downloads/ |
| Unwarp | `Toolbox for estimation and removal of movement-by-susceptibility induced variance in fMRI time series' | [Andersson, 2001], http://www.fil.ion.ucl.ac.uk/spm/toolbox/unwarp.html |
| xjView | SPM2 visualization | http://people.hnl.bcm.tmc.edu/cuixu/xjView/ |
| Zephyr | SPM2 batch for preprocessing | http://diddy.dartmouth.edu/zephyr/ |
Table 14 shows software in connection with neuronal modeling. [De Schutter, 1992] is an early review of seven neuronal modeling software: AXONTREE, GENESIS, NEURON, NEMOSYS, NODUS, SABER and SPICE. GENESIS and NEURON are probably the most widely used. See also the sort review of [Jeong, 2005].
| Name | Impl. | Description | Reference |
| 4D Toolbox | Matlab | Analysis and visualization of (Neuromag) MEG data | http://boojum.hut.fi/~ojensen/4Dtools/ |
| ASA | Windows(?) | ``Advanced source analysis''. EEG or MEG analysis with source analysis from ANT. | http://www.ant-software.nl/asa/ |
| BESA | Windows | ``Brain Electrical Source Analysis''. Commercial EEG and MEG source localization. | http://www.besa.de/ |
| Brain project (bp) | Windows, Linux | ``a Delphi Library for EEG data Analysis and Display'' | http://www.irisa.fr/siames/GENS/mcongedo/MC_Projects.html |
| BrainStorm | Matlab | MEG and EEG data processing, visualization and source localization | http://neuroimage.usc.edu/brainstorm/ |
| CogniTrace | Linux | ``EEG/ERP data acquisition for 32 to 128 channels'' from ANT. | http://www.ant-software.nl/erp/ |
| Curry | PC, HP, Sun, SGI | Commercial program from Neuroscan with electromagnetic source localization and visualization | http://www.neuro.com/product.sstg?id=39 |
| cvapp | Java | Neuronal morphology editor | http://www.cns.soton.ac.uk/~jchad/cellArchive/cellArchive.html |
| EEGLAB | Matlab | Analysis (independent component analysis) and visualization for EEG and MEG by Arnaud Delorme and Scott Makeig from Swartz Center for Computational Neuroscience et al. | http://sccn.ucsd.edu/eeglab/ |
| EEG toolbox | Matlab | EEG toolbox for visualization | http://eeg.sourceforge.net/ |
| ERPWAVELAB | Matlab | Analysis of event related EEG and MEG data in the time-frequency domain. | [Mørup et al., 2007], http://www.erpwavelab.org/ |
| G-clamp | LabView | http://hornlab.neurobio.pitt.edu/ | |
| ILAB© | Matlab | Eye movement analysis software for data generated by ISCAN©and ASL© | [Gitelman et al., 2001], http://www.brain.northwestern.edu/ilab/ |
| Klusters | Linux | ``A graphical interface for spike sorting of extracellular neuronal recordings'' | http://klusters.sourceforge.net |
| LOFA | [Gokcay et al., 1999] | ||
| LORETA | ``Low Resolution Brain Electromagnetic Tomography''. Program for inversion reconstruction of the 3D electromagnetic distribution from surface EEG and MEG recordings. | [Pascual-Marqui, 1999], http://www.unizh.ch/keyinst/NewLORETA/LORETA01.htm | |
| NeuroBench | Java | Program to analyze and view electrophysiological recordings | http://www-hbp.usc.edu/Projects/neuronBench.htm |
| NeurolucidaTM | Commercial software from MicroBrightField for neuroanatomical analysis, e.g., 3D neuron reconstruction. | [Glaser and Glaser, 1990] http://www.microbrightfield.com/prod-nl.htm | |
| NeuroModeller | Windows | 3D Visualization, 3D model generation from contours | http://users.infohouse.com/amiller/ |
| NeuroScholar | Java | MySQL Database frontend with management of bibliography, histological and tracing data. | [Burns, 2001,Burns, 1998,Shahabi et al., 1999,Burns et al., 2002,Burns et al., 2003], http://www.neuroscholar.org, http://chasseur.usc.edu/ns/ |
| NeuroScope | C++, Linux/KDE | ``Viewer for electrophysiological and behavioral data with limited editing capabilities'' | http://neuroscope.sourceforge.net |
| NeuroSim | Matlab | ``Neurosim is a MATLAB program that implements a conductance-based model sympathetic neuron and can also can create synaptic template files for driving G-clamp'' | http://hornlab.neurobio.pitt.edu/ |
| SOURCE | Commercial EEG dipole source localization from Neuroscan | http://www.neuro.com/product.sstg?id=40 | |
| Spike2 | Windows | Commercial software for data capture and analysis of, e.g., electroneurophysiological data made by Cambridge Electronic Design. | http://www.ced.co.uk/spk4wglu.htm |
| TEMPO | OpenGL | 3D EEG scalp data plotting | http://tempo.sourceforge.net/ |
| XANAT | X Windows | Analysis and storage of neural connectivity data | [Press et al., 2001b,Olshausen and Press, 1994], http://redwood.ucdavis.edu/bruno/xanat/xanat.html |
http://www.compneuro.org/ includes CD-ROM that is included in connect ion with the book Computational Neuroscience: Realistic Modeling for Experimentalists [Schutter, 2000].
Finn Årup Nielsen 2010-04-23