Where Are Talairach Template In Spm Matlab Fmri

SPM Extensions

Introduction

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

If you lot discover inaccuracies or out of date links, delight electronic mail the SPM manager. Too, to have your SPM extension linked here, send an email including a URL, a contact email, and a brief summary (please notation 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. Delight contact the respective extension authors with questions and issues (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 equally an RSS feed.

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

Quick Links

Toolboxes:

Utilities:

Batch Utilities:

Templates:

AAL - Anatomical Automated Labeling SPM12 SPM8 SPM5 SPM2 SPM99

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

Author: Gin

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

AAL2 - Anatomical Automatic Labeling two SPM12

Summary: Implementation of a new parcellation of the orbitofrontal cortex in the automatic 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.

Writer: Rolls, Huang, Joliot

URL: https://world wide web.gin.cnrs.fr/en/tools/aal/

Acrid - Artefact correction in diffusion MRI SPM12 SPM8

Summary: The Artefact correction in improvidence MRI (Acid) toolbox is an academic software toolkit for pre-processing of improvidence MRI information, estimation of DTI indices and normalisation of DTI index maps, which fully integrates into the batch system of SPM8.

Author: Siawoosh Mohammadi

URL: http://world wide web.diffusiontools.com/

AICHA - An atlas of intrinsic connectivity of homotopic areas SPM12

Summary: An atlas of intrinsic connectivity of homotopic areas, equally 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 depiction and spatial normalization for patients with encephalon damage. It uses the unified normalisation-segmentation algorithm with an explicit extra prior for the lesion that is refined iteratively in a patient-specific style. Lesions are then divers as a prepare of outlier voxels while taking into account the typical variability in anatomy in salubrious controls. ALI can likewise generate lesion overlap maps.

Author: Mohamed Seghier

URL: Contact electronic mail above

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. Information technology is designed to respond the frequently asked question: what the *?%! does that bit practice?

Author: Antonia Hamilton

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

AQuA SPM5

Summary: AQuA is a tool that helps you in the assessment procedure for the quality of the caused fMRI data, identifying images with movement and other artefacts, so that they do not compromise the experimental assay.

Author: Antonios Antoniou and Juan J. Lull

URL: http://world wide web.ibime.upv.es/mi/

aslm - a slightly modified asl-module SPM8

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

Author: Philipp Homan

URL: http://aslm.sourceforge.internet

ASLtbx SPM12 SPM8 SPM5 SPM2

Summary: ASLtbx is a Matlab and SPM based toolkit for processing arterial spin labeling (ASL) perfusion MRI data. It'southward basically a collection of a agglomeration of batch scripts. I'm currently only distributing the SPM5-based version, just the SPM2(or 8)-based version tin exist obtained through e-mail. The function for quantifying cognitive claret period should exist SPM contained except the image reading and writing functions from SPM.

Writer: Ze Wang

URL: http://world wide web.cfn.upenn.edu/~zewang/ASLtbx.php

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 packet, we present Alzheimer'southward Disease Score (ADS) adult using Support Vector Machine for Alzheimer's disease research. ADS used ADNI database in N America as its training data. With this software, we too hope to streamline VBM analysis for the usability in clinical settings.

Author: Akihiko Shiino

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

BFAST3D - Bayesian Fast Accurate Spatial Tricks in 3D SPM12

Summary: Extends SPM's Bayesian single-discipline fMRI assay to permit for estimation by MCMC and the Spatial VB method as described in Siden et al. (2016).

Writer: Per Siden

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

BrainNet Viewer

Summary: BrainNet Viewer is a brain network visualization tool, which tin can help researchers to visualize structural and functional connectivity patterns from dissimilar levels in a quick, like shooting fish in a barrel, and flexible way.

Writer: 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 Centre(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/

BrainSlicer

Summary: BrainSlicer is a control-line prototype viewer. Its main purpose is to produce high-quality publication-set up figures. Main functionalities include: (1) possibility of overlaying multiple images with adjustable opacity, (2) thresholding and clusterization of each layer, (three) visualize colorbar for each desired layer, (4) handy visualization of p-value maps as (ane-p), and (v) effectually 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, encephalon spontaneous activity, functional connectivity analysis, complex network analysis, statistical assay and results visualization. A universal input/output interface was designed for about functions, and users tin customize their own scripts into GUIs by calculation a few lines of MATLAB code. We've too implemented efficient file loading/saving functions and parallel calculating scripts using matrix operations, OPENCL and multithreading to speed upwardly 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 surround. The coordinate-based search is performed using Finn Aarup Nielsen's Brede Database. Works with coordinates in Talairach and MNI infinite, MNI-to-Talairach transformations are available (Brett and Lancaster transformations). Moreover, query results tin can be exported automatically to the suitable bibliographic file format (BibTeX, Reference Director, RefWorks, EndNote).

Writer: Bartlomiej Wilkowski

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

bspmview SPM12 SPM8

Summary: Another SPM viewing programme. Intuitive and customizable user interface for exploring statistical images (e.g., spmT*), including display of positive and/or negative furnishings; voxel- and cluster-level thresholding; instant anatomical labeling; and customizable color maps. Hands generate customizable surface renderings. Salve thresholded whole-brain maps, specific clusters, and ROIs. View results tables interactively, and save publication-ready tables. Although congenital for viewing statistical images, it allows viewing other image types (e.m., contrast/mask/ROI images).

Writer: Bob Spunt

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

Computational Anatomy Toolbox SPM12

Summary: This toolbox provides diverse morphometric methods for computational anatomy such equally voxel-based morphometry (VBM), surface-based morphometry (SBM), deformation-based morphometry (DBM), and region- or characterization-based morphometry.

Author: Christian Gaser and Robert Dahnke

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

CCA-fMRI SPM5 SPM2

Summary: The CCA-fMRI utilizes approved correlation analysis in combination with the Airship model and adaptive filtering of fMRI data to detect areas of brain activation. The CCA-fMRI toolbox provides its own user interface and tin can also be used as stand solitary scripts, e.m. for batch processing.

Writer: Magnus Borga

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

Form - Classifier Learning for Asymmetrically Small Samples SPM8

Summary: Multivariate kernel-based design classification using support vector machines (SVM) with a novel modification to obtain more balanced sensitivity and specificity on unbalanced data-sets (i.due east. those with very different numbers of cases in each group).

Writer: Ged Ridgway

URL: Contact email to a higher place

Complexity SPM8

Summary: Complication 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, Cantankerous Approximate Entropy, Multiscale Sample Entropy and Wavelet MSE, are available to calculate the entropy. Matlab toolbox, "Tools for NIfTI and Clarify paradigm", is needed.

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

URL: http://loft-lab.org/index-v.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. Showtime-level univariate and multivariate regression and bivariate and semipartial correlation connectivity measures. Seed-to-voxel and ROI-to-ROI analyses. Second level random upshot analyses. Gui and batch processing.

Writer: Alfonso Nieto-Castanon

URL: https://world wide web.nitrc.org/projects/conn

ConnExT - Connectivity Explorer Toolbox SPM8

Summary: Easy style to visually explore the bespeak time series and the functional connectivity map of fMRI data. At that place are diverse processing options that tin be applied to the time serial, and the effect is apace seen. A seed region tin can also be chosen without difficulty for functional connectivity analysis, and the correlation coefficients map is instantaneously displayed. GUI and batch processing.

Writer: Guilherme Coco Beltramini

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

fMRI CPCA

Summary: Constrained Principal Component Analysis (CPCA) combines regression analysis and master component analysis into a unified framework. This method derives images of functional neural networks from atypical-value decomposition of BOLD bespeak time serial, 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

DAiSS SPM12

Summary: SPM12 toolbox for Information Analysis in Source Space (beamforming, minimum norm and related methods), developed by collaboration of UCL, Oxford and other 1000000 centres.

Author: Vladimir Litvak

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

DICOMCD Import SPM5

Summary: This toolbox can import a Siemens DICOMCD (maybe other scanners too) to local storage without being dislocated nigh which dicom file belongs to which session. By analyzing the DICOMDIR file, all data is saved in dicom format, merely split according to subject and sequence. It tin can also catechumen Siemens DICOMCD or imported information to NIFTI files without having to modify directory multiple times.

Author: Pieter Vandemaele

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

Diffusion Ii - Mail-processing for diffusion weighted image serial SPM12 SPM8 SPM5 SPM2

Summary: Mail-processing for diffusion weighted paradigm series. Functionality includes movement correction for prototype time serial, 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 Banana for Resting-Land fMRI SPM8 SPM5

Summary: DPARSF is a convenient plug-in software based on SPM and Residuum. Y'all just need to arrange your DICOM files, and click a few buttons to set parameters, DPARSF volition and then give all the preprocessed (slice timing, realign, normalize, polish) data, FC, ReHo, ALFF and fALFF results. DPARSF tin can besides create a report for excluding subjects with excessive caput motility and generate a set of pictures for easily checking the consequence of normalization. You lot can utilize DPARSF to extract AAL or ROI time courses (or excerpt Gray Matter Volume of AAL regions, command line only) efficiently if you lot want to perform pocket-size-world assay. DPARSF basic edition is very easy to use, just click on buttons if you are non certain what information technology ways, popup tips would tell you what you demand to do. DPARSF advanced edition is much more than flexible, you lot tin can use it to reorient your images interactively or define regions of interest interactively. You tin can skip or combine the processing steps in DPARSF advanced edition freely.

Writer: 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 place the frequencies of cardiac- and respiration-induced racket, so eliminate them from the brain data. The toolbox can be operated both in graphical and batch mode.

Author: Arno Solin and Simo Sarkka

URL: http://becs.aalto.fi/en/inquiry/bayes/drifter/

EEG Analyzer SPM12

Summary: The "EEG Analyzer" toolbox for SPM provides a user-friendly interface for One thousand/EEG visualization. Information technology 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

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. Information technology includes preprocessing, physiological noise correction, OLS and GLS analysis, as well as quantification of perfusion.

Author: Luis Hernandez

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

fECM - Fast eigenvector axis 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 style to control the algorithm is by calling the 'fegui' role which brings up a menu where fMRI information, 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/main/matlab/fastECM

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 fourth dimension-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing.

Author: Robert Oostenveld

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

fMRIPower SPM8 SPM5

Summary: This tool is based on the work outlined in Mumford & Nichols, NeuroImage, 39(one):261-8, 2008. Basically y'all 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 ability calculation is done for y'all.

Author: Jeanette Mumford

URL: http://fmripower.org/

gPPI SPM8

Summary: An automatic 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 truthful 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.

Writer: 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 encephalon 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 - Filigree Code Assay Toolbox SPM12

Summary: The GridCAT allows users to behave 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, tin edit the open-source lawmaking accompanying the GridCAT to implement their own analysis pipelines. An example dataset is provided together with a detailed manual, so that users tin can explore the GridCAT's functionality.

Writer: 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(Cognitive Claret Menstruation) data assay. This toolbox is run and tested on SPM8 with MATLAB 7.6.0 (R2008a) under Linux. Theoretically, most of the functions (except the outset ii menus which are especially designed for the Batch Editor of SPM8) of this toolbox should exist compatible with SPM5 and should also work smoothly under the Windows Bone. Read the manual in the package for more details.

Author: Senhua Zhu, Hengyi Rao and Siyuan Hu

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

hMRI-toolbox SPM12

Summary: The hMRI-toolbox (Tabelow et al. 2019) is an like shooting fish in a barrel-to-apply open-source and flexible tool, for quantitative MRI (qMRI) data treatment and processing. Information technology 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 hands combined with existing SPM toolboxes for estimating improvidence MRI parameter maps, and information technology 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 depiction of subcortical brain structures. They are cardinal input parameters for biophysical models designed to guess tissue microstructure properties such as the MR yard-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.

Writer: 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 beefcake space. Through this set of routines is able to compute the volume of gross anatomical structures. Other facilities are related to the ciphering of the SPAMs (Statistical Probability Anatomy Maps) and MaxPro (Maximum probability) maps that tin exist used in classification procedures. Also the ciphering of the gray matter, white affair, 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.

Writer: Lester Melie Garcia and Yasser Aleman-Gomez

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

iBrain assay toolbox SPM8 SPM5 SPM2

Summary: The iBrain analysis toolbox for SPM is a free toolbox that provides an automatic processing pipeline for diverse single- or multi-subject area 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.eastward. before any processing is really 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 rest of action between 2 regions of interest is typical or atypical, based on statistical comparison between an private and a group of controls. The toolbox displays laterality index (LI) plots equally a function of an adaptive threshold, and provides statistical cess of the plots to determine lateralisation.

Writer: David Abbott

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

IBZM-tool - Practiced 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 move correction), stereotactical normalization, scaling, VOI-analysis of striatal IBZM uptake, nomenclature of striatal IBZM-uptake, and standardized display.

Writer: 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-land networks or RSNs) past describing fMRI activation maps or other statistical maps in role-oriented, objective and quantitative way using a set of xv metrics conceived to quantify the degree of 'engagement' of ICNs for any given statistical map of involvement. 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), likewise.

Author: Lajos R Kozak

URL: https://world wide web.nitrc.org/projects/icn_atlas/

ISAS - Ictal-Interictal SPECT Analysis by SPM SPM2

Summary: ISAS analyzes the divergence 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 information 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. Information technology 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 characteristic maps encoding information about which voxels are likely to correspond to missing and abnormal tissue. The characteristic maps are input as predictors to a fully trained and cantankerous-validated Gaussian Naive Bayes classifier to obtain predictions about which voxels correspond to lesioned tissue. Elementary post-processing (smoothing and cluster thresholding) tin be applied to reduce the occurrence of imitation positives. No command grouping is necessary for lesion. The toolbox includes the option for obtaining and post-processing individual patient lesion predictions entirely via a unproblematic dialogue-based interface, and besides includes examples scripts for running batch jobs.

Author: Joseph Griffis

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

LI-toolbox SPM12 SPM8

Summary: Allows assessment of laterality effects in imaging information using diverse thresholding options. Amidst other features, regionally-restricted analyses are possible and a bootstrapping arroyo allows to assess data homogeneity to reduce the effect of outliers. The toolbox can now be scripted and batched, allowing for unattended analyses.

Writer: 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 information. 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.zilch

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) information. It includes classical, information-theoretic and Bayesian measures of model quality also equally 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 division and filtering to deal with hyper intense white affair and enlarged ventricles, mutual in scans of premature neonates.

Writer: Richard Beare

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

MARINA - MAsks for Region of Involvement 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 encephalon published by Tzourio-Mazoyer et al. (2002). Voxel coordinates of brain structures come from their SPM toolbox AAL (automatic 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 East-footstep of the algorithm, not just as a post-processing step. Compared to the New Segment, the resulting segmentation is shown to exist more than smooth and with less discontinuities, while at the aforementioned fourth dimension the accuracy is not significantly inverse.

Writer: Yu (Andy) Huang

URL: http://world wide web.parralab.org/mars/

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

Summary: Region of involvement (ROI) analysis, including ROI definition, combination of ROIs with simple algebra, extraction of information for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics mechanism.

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". Ane of the benefits of masked dissimilarity images is an improved spatial precision, particularly if smoothed / low resolution image data were analyzed (e.thou. betwixt-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 pattern of the toolbox is modular, then it tin 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 automated method that finds an optimal threshold for binarising an average epitome. Also offers a more flexible method (without GUI) for skillful control over the mask.

Author: Ged Ridgway

URL: http://world wide web.cs.ucl.air conditioning.britain/staff/k.ridgway/masking

MM - Multivariate Methods for fMRI SPM5 SPM99

Summary: Implements several multivariate methods for fMRI data analysis, including master components analysis (PCA), projected PCA, multivariate linear model (MLM) and fractional least squares (PLS). Useful for both exploratory and confirmatory analyses.

Author: Ferath Kherif

URL: Contact email to a higher place

MP2RAGE SPM12

Summary: This extension is related to MP2RAGE sequence. The commencement job removes the racket groundwork of the UNI prototype, helping for segmentation. To make up one's mind the regularization parameter, an interactive version of the job shows the furnishings of the chosen parameter value in existent time. The second job allows to judge 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 Organisation.

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 blueprint, 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 seven.3 running in Fedora Core 6 linux.

Author: Simo Vanni

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

MRTOOL - Toolbox for structural MR imaging analyses SPM12

Summary: In view of the increasing availability of MR imaging information 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. (i) 'T1-w/T2-w image' for the generation of the multimodal ratio epitome. (2) 'Optimized Bias Correction parameters' for the definition of the optimal prepare of input parameters (regularization and FWHM) required during the bias correction of MR images in SPM12. (3) 'Encephalon Extraction' for the generation of skull-stripped images. (4) 'Optimized Normalization' for an enhanced spatial registration and partition of elderly subjects characterized past a marked ventricular enlargement and advanced atrophy.

Writer: Marco Ganzetti

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

NIRS-SPM SPM12 SPM8 SPM5

Summary: NIRS-SPM is a statistical parametric mapping toolbox for near-infrared spectroscopy. Based on general linear model and Lord's day'south tube formula, NIRS-SPM non merely provides activation maps of oxy-, deoxy-, and full- hemoglobin, but as well allows for the super-resolution activation localization.

Author: Jong Chul Ye & Sungho Tak

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

NPBayes-fMRI

Summary: Convenient 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 nether not-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'due south FMRISTAT software. Also provides cluster p-values for F images (with or with out an assumption of stationarity).

Writer: Satoru Hayasaka

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

PETPVE12 - Partial Volume Effects correction of PET images SPM12

Summary: This toolbox implements two popular algorithms for fractional volume correction (PVC) of PET images within an piece of cake to employ 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 information technology requires no permutation tests.

Author: Tamas Spisak

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

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 of measurement at CIMES (FGUMA)

URL: http://world wide web.uimcimes.es/contenidos/golink?p=1

Residual - Resting-land fMRI information assay toolkit SPM8 SPM5 SPM2 SPM99

Summary: Remainder is an independent toolkit designed for resting country fMRI data assay. It eases the analysis procedure 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, assuasive rigid registration of 3D multi-modal images based on simultaneous sectionalisation, 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 fourth dimension courses averaged across subjects from within 2d level (random effects) analyses. The toolbox offers a large diverseness of plot configuration both suitable for data exploration and producing loftier quality figures for publications.

Author: Jan Glascher

URL: http://rfxplot.sourceforge.internet/

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

Summary: This toolbox implements an approach to find 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 racket 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

rsHRF - resting state HRF interpretation and deconvolution SPM12

Summary: This toolbox is aimed to remember the onsets of pseudo-events triggering an hemodynamic response from resting land fMRI BOLD voxel-wise betoken. It is based on point process theory, and fits a model to call up the optimal lag between the events and the HRF onset, as well equally the HRF shape, using either the canonical shape with two derivatives, or a (smoothed) Finite Impulse Response. In one case that the HRF has been retrieved for each voxel, it tin can exist deconvolved from the time serial (for instance to improve lag-based connectivity estimates), or one tin 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 footling user input. Particularly suited for situations when the number of conditions and timing of the events vary among subjects, such as in EEG-fMRI assay. When the onset and elapsing 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/Condom

SAMIT - Small Creature Molecular Imaging Toolbox SPM12 SPM8

Summary: The aim of this toolbox is to facilitate the structure 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/

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 every bit 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 i) track the boilerplate excitatory Ae, slow and fast inhibitory synaptic gains, B and G, by automatically fitting EEG information to a neural mass model; 2) compute four synaptic gain ratios (excitatory/deadening inhibitory Ae/B, excitatory/fast inhibitory Ae/One thousand, excitatory/(dull + fast) inhibitory Ae/(B+Thou), and irksome/fast inhibitory ratio B/M, and smoothen them using moving boilerplate filter; 3) display the path to epilepsy through the synaptic gain space.

Author: Xiaoya Fan, Rudy Ercek & Antoine Nonclercq

URL: https://world wide web.researchgate.net/publication/347523446_Synaptic_Gains_Tracking_Toolbox

SPM EEG Spike detection toolbox SPM12

Summary: SpikeDet is a fully automated method of interictal spike detection in an EEG tape 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. (ii) Detected spikes are separated into clusters. (3) The number of clusters is automatically adjusted. (four) Centroids are used as templates for more specific spike detections, therefore adapting to the types of spike morphology. (five) Detected spikes are summed.

Author: Antoine Nonclercq & Rudy Ercek

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

SPMd - Statistical Parametric Mapping Diagnosis SPM5 SPM2 SPM99

Summary: Allows yous to establish the validity of inferences in fMRI modeling through diagnosis of linear model assumptions, and to characterize fMRI indicate and artifacts through exploratory data analysis.

Writer: 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 up and employ 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://world wide web.spmmouse.org/

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

Summary: This toolbox implements the multivariate Scaled Subprofile Modeling (SSM) method based on Master Component Analysis (PCA). It tin can generate spatial covariance patterns from functional or anatomical encephalon 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 meridian inference inference on polish random fields. Information technology implements the methods, comparison simulations to SPM12, and data analysis equally reported in Schwartzman and Telschow (2018).

Writer: Fabian Telschow and Armin Schwartzman

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

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.

Writer: Joern Diedrichsen

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

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

Summary: SwE is a toolbox to arrange general repeated measures and longitudinal data. It makes no supposition nigh counterbalanced designs and, through the utilize of a "marginal model", allows either between- or within-subject variables (e.g. in 1 longitudinal pattern, you tin model both time and gender). Variance (& covariance) are estimated separately for each group. It has accurate parametric results that work reasonably well for at to the lowest degree twenty subjects per group, and otherwise a bootstrap resampling inference procedure (that additional provides FWE voxel- or cluster-wise inferences).

Writer: 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 design analysis (MVPA) of functional and structural MRI information. TDT provides an interface to SPM which obviates the need to manually specify preparation and examination 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 information using peripheral measures of respiration and cardiac pulsation. It incorporates noise models of cardiac/respiratory phase (RETROICOR, Glover et al. 2000), as well as middle rate variability and respiratory volume per fourth dimension (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 direct 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, information technology allows to statistically isolate the influence of external variables of interest on brain construction. 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. Information technology writes SPM2-compatible data and now includes an selection 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 (near) any existing statistical (parametric) SPM design for 3D volume or surface data.

Writer: 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 just needs to select the raw functional and structural NIfTI files from the subjects. The graphical user interface makes the processing and analysis options attainable for neuroscientists, with reasonable choices of default settings. UF2C allows the user to report functional connectivity both through a quantitative view that provides detailed values of average connectivity, and through a spatial view that provides statistical maps that tin be directly used for farther analyses. All results are carefully organized in singled-out folders for each subject field, 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 motion-by-susceptibility induced variance in fMRI fourth dimension series. Allows inclusion of a measured field map which can be processed by the FieldMap Toolbox. Delight note that for SPM5 and higher up, the Unwarp is part of the SPM distribution.

Author: Jesper Andersson & Chloe Hutton

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

VDB SPM12 SPM8

Summary: The software parcel VDB 1.0 has been designed for analysis neural activities of encephalon 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 bundle had been tested in Windows seven/Windows 10(32 and 64 scrap) platforms. This software uses the 4D NIFTI-i file format for the epitome data. All images must be written as 4D NIFTI-i. All data must be preprocessed by using SPM earlier these data tin exist processed utilizing the software bundle VDB1. 0.

Writer: Guang-Yu Zhang & Hua Ma

URL: https://world wide web.nitrc.org/projects/vdb/

Volumes Toolbox SPM12 SPM8 SPM5 SPM2

Summary: This toolbox contains various functions that deal with epitome volumes. Utilities include tools for splitting and combining volumes (for when multiple measurements are recorded per slice), extracting fourth dimension 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 piece of work in any SPM version, just information technology requires Linux / Unix or Mac Os.

Writer: Erick J. Canales-Rodriguez

URL: http://world wide web.wbmorphometry.com/

Wavelet-based SPM SPM8 SPM5 SPM2

Summary: A new framework for the detection of brain activity from fMRI information 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 infinite (encounter Atlas Modifications under Technical Notes). Additional atlases tin can be added without much difficulty. The toolbox was developed in the Functional MRI Laboratory at the Wake Forest Academy School of Medicine.

Writer: Joseph Maldjian

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

xjView - Viewing tool SPM12 SPM8 SPM5 SPM2

Summary: A viewing programme for SPM. p-value slider, piece viewer, displays multiple images at a time, display both positive and negative contrast at a fourth dimension, beefcake description with a single mouse click, etc.

Author: Xu Cui, Jian Li, Xiaowei Vocal

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

XMLTools SPM2

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 Dominicus, LINUX, and Microsoft Windows operating systems. The toolbox has been used to capture PET and fMRI analysis results and the associated analysis model specifications.

Writer: David Keator

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

ASLtbx SPM8

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 ii. The function for quantifying cerebral claret flow should be SPM contained except the prototype reading and writing functions from SPM. In our website, you lot can notice instance 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 exist posted in https://groups.google.com/forum/#!forum/asltbx-word-lath.

Author: Ze Wang

URL: http://world wide web.cfn.upenn.edu/~zewang/ASLtbx.php

BENtbx SPM8

Summary: BENtbx (Encephalon Entropy Mapping Toolbox) is a Matlab and SPM based toolkit for brain entropy mapping using fMRI data. Entropy is calculated using Sample Entropy (SampEn). Considering of the optimized SampEn calculation and C++ based implementation, a whole brain BEN mapping tin can exist as fast as 3 seconds, compared to >7 hours using the included Matlab code. Sample data is provided in the same webpage.

Writer: 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 Homo Brain Mapping newspaper. Sample lesion data and behavior data are provided to facilitate the use of SVR-LSM toolbox.

Writer: Ze Wang

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

Utilities

AveLI SPM12 SPM8 SPM5

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

Author: Kayako Matsuo

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

BrainMagix SPM Viewer SPM8 SPM5

Summary: A free, professional viewer for SPM fMRI activations. Coffee-programmed, cross-platform (Windows, MAC, Linux), without Matlab license, making information technology 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 wing 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://world wide web.imagilys.com/brainmagix-spm-viewer/

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

Summary: Tools from the Cognitive Brain Mapping Grouping (Northwestern Academy) 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.

Writer: Darren Gitelman

URL: http://www.encephalon.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 past calculating the amount of factor variance that is besides accounted for past the other factors in the blueprint (expressed in R^2). Essentially, the higher R^2 is, the lower the t-values will exist. Also tin calculate (and create) the virtually 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

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 institute. Can be used interactively or scripted.

Author: Tom Nichols

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

Fluctuation - Chore-contained 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 not-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. Vanquish scripts for image management, .... and a few other tools.

Author: Luis Hernandez

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

log_roi_batch - Script for ROI value extraction SPM8 SPM5

Summary: log_roi_batch creates tables of mean or standard divergence for regions of involvement (ROIs) or counts voxels with values within a given range. Voxel exclusion criteria can be specified, which tin can besides 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-serial 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 packet offers a standalone implementation of multiple comparison correction for fMRI information. Information technology achieves this through a permutation testing arroyo which controls familywise mistake 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 costless 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

mri_toolbox - Analyze read/write utilities SPM99

Summary: A matlab toolbox for reading, writing and viewing Clarify slices and volumes. It provides endian conversions and simple options for orthogonal reslicing. The GUI requires at least Matlab six.0 but I/O functions should work nether matlab 5.10.

Author: Darren Weber

URL: http://eeg.sourceforge.internet

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

Summary: Plug in for SPM's spm_orthviews (accessed from "Check Reg" push button). From pop-up card can reorient, visualize diffusion tensors, use a motion-picture show 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 cypher 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 ways 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://world wide web.nitrc.org/projects/ppi_batch_hipp/

pvconv.p - A Bruker information converter SPM99

Summary: Converts Bruker format MRI data to Clarify or MINC epitome format; based on converters past Andrew Janke (MINCtools).

Author: Matthew Brett

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

r2agui - A Philips PAR/REC to Clarify/NifTI information converter SPM5 SPM2

Summary: Automatically batch-converts V3 (Philips Intera scanner family) and V4 (Philips Intera scanner family) data formats to Analyze 7.v or NIfTI ane.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 case is used to illustrate potential pitfalls and solutions.

Author: Douglas Steele

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

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

Summary: Computes slicewise browse by scan difference and standard deviations. Useful to examine quality of image timeseries. Scans or slices that testify deviations from timeseries mean may be decadent and need more than detailed inspection.

Writer: Matthew Brett, Volkmar Glauche

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

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

Summary: A drove 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 epitome visualization SPM8 SPM5

Summary: Utility that will (1) plot histograms of voxel values in an SPM, (2) brandish a surface plot of voxel values at a detail axial slice, or (3) display a besprinkle plot and calculate a Pearson correlation of values in corresponding voxel locations between two SPMs.

Writer: Rob Ellis

URL: http://tools.robjellis.net

Batch Utilities

aa - Automatic Analysis SPM8 SPM5

Summary: An easy-to-use scripting organization. Cull a default recipe and preprocess all your data with just 7 lines of matlab. Add together further lines to override the default processing parameters or modify pathway. Modular design, like shooting fish in a barrel to program. Restartable - if information technology crashes, merely rerun and it will first where information technology left off. Benchmarking facility. Easy to update as modules are stored centrally.

Author: Rhodri Cusack

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

AutoSPET SPM5

Summary: AutoSPET (Automated SPM tool invocation for PET analysis images), is a useful graphical user interface to improve efficiency in running SPM experiments. Information technology 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. Information technology tin and then be used to run automated analysis in batch. The batch file would be helpful in automating the labeling process and can be integrated in a full analysis (pre-processing, start level, results and labeling). The batch script can be evoked from spm8 batch interface. In batch interface: SPM > Tools > AAL.

Writer: Atesh Koul

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

parallelize_matlabbatch SPM8

Summary: This script loads selected SPM batch, tries to intelligently guess which fields are potential candidates for "parallel splits" and later on interactively asking for confirmation splits your batch into multiple .mat, .m and .sh files (placing them in the aforementioned directory as the original batch) - the latter existence ready for submission to Sun Grid Engine queue. Splits are done ane:1, meaning that all the fields y'all select must have the same size. Tested with: NewSegment, Run DARTEL (existing Templates) and Normalize to MNI Infinite.

Author: Stanislaw Adaszewski

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

spm_segment SPM5 SPM2 SPM99

Summary: A GUI and control line interface to measure GM/WM/CSF volumes from a series of 3D volume images. Pick 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.air-conditioning.uk/cloudburst/index.html

SPMJobs12 SPM12

Summary: Batch process multiple subjects' fMRI data by running a single control up to the showtime level analysis; separate files into each processing pace; generate job files beforehand for you to double-check and review; save informative graphs as pdf for quality control; can transport e-mail notification when a job is done.

Author: Jerry Zhu

URL: http://zhupsy.com/more than

spm2-batch SPM2

Summary: Batch engine for SPM2. Includes basic preprocessing, model estimation, dissimilarity setup, group stats. Runs multiple session designs. Tested on Linux and Windows XP, matlab 6.5. An case analysis setup script is provided.

Writer: Bas Neggers

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

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 field) are supported, e.chiliad. preprocessing of fMRI data, first-level statistics, prototype calculator, bank check registration, jobs with external SPM toolboxes.

Writer: 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 2d level analysis. spmjob has both flexible scripting support and a user friendly GUI.

Author: Thomas Tanner

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

Templates

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

Summary: An advisable [18F]FDG PET brain healthy control (HC) dataset is mandatory to reach adept functioning in voxel-wise image analyses, peculiarly on a single bailiwick basis. Here is provided a [18F]FDG PET brain dataset of HC based on data nerveless by the Italian association of nuclear medicine, for the extraction of voxel-based encephalon metabolism maps. The performance of this HC dataset was tested in comparison with other standard reference HC datasets (encounter 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 unmarried-subject level, fix-to-use in enquiry 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.information technology/brain-fdg/

B2K template images for neuroimaging in birdie SPM99

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

Writer: Kevin Black

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

Canine Brain Atlas

Summary: T2w datasets were acquired from xvi neurologically camouflaged 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 grayness (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 encephalon template.

Author: Bjorn Nitzsche

URL: http://beast-brain-mapping.com/canis familiaris

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 grouping 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 (Information technology); Vrije Universiteit Medical Eye, Amsterdam (NL); Technische Universitet Munich, Munich (GE); and Hopitaux de Marseille, Marseille (FR).

Writer: Pasquale Anthony Della Rosa & Daniela Perani

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

Ovine Brain Atlas

Summary: The ovine, unbiased, population-averaged standard magnetic resonance imaging template brain book: 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 prototype. See Nitzsche et al, Frontiers in Neuroanatomy, 2015, for more details.

Author: Bjorn Nitzsche

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

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 infinite are also available. Additionally, a technical report is included. A newspaper by McLaren et al. is in printing at NeuroImage.

Writer: 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.

Writer: Kevin Blackness

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

UNC 0-1-2 Infant Atlases

Summary: In that location are 3 atlases defended for neonates (T2), 1-twelvemonth-olds (T1), and 2-year-olds (T1). Each atlas comprises a set up of 3D images fabricated upwardly of the intensity model, tissue probability maps, and anatomical parcellation map.

Author: Feng Shi

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

Where Are Talairach Template In Spm Matlab Fmri,

Source: https://www.fil.ion.ucl.ac.uk/spm/ext/

Posted by: leclairformar.blogspot.com