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https://github.com/spm

Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.

Proper citation: SPM (RRID:SCR_007037) Copy   

•   Source: SciCrunch Registry

http://inlab.ibfm.cnr.it/PET_template.php

This is a place holder for this tool. The documentation is not yet available (documented 5/30/2014).

Proper citation: Dementia-specific FDG PET Template for SPM analyses (RRID:SCR_010465) Copy   

•   Source: SciCrunch Registry

http://www.diffusiontools.com/documentation/poas.html

Software toolbox for SPM to denoise diffusion MRI data. Used for diffusion weighted magnetic resonance imaging data enhancement based on structural adaptive smoothing in both voxel space and diffusion-gradient space.Part of the ACID-toolbox.

Proper citation: POAS4SPM (RRID:SCR_010469) Copy   

•   Source: SciCrunch Registry

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

MATLAB toolbox for deep-brain-stimulation (DBS) electrode reconstructions and visualizations based on postoperative MRI and computed tomography (CT) imaging. The toolbox also facilitates visualization of localization results in 2D/3D, analysis of DBS-electrode placement's effects on clinical results, simulation of DBS stimulations, diffusion tensor imaging (DTI) based connectivity estimates, and fiber-tracking from the VAT to other brain regions (connectomic surgery).

Proper citation: LEAD-DBS (RRID:SCR_002915) Copy   

•   Source: SciCrunch Registry

https://github.com/lrq3000/spm_auto_reorient_coregister

Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12.

Proper citation: spm_auto_reorient_coregister (RRID:SCR_017281) Copy   

•   Source: SciCrunch Registry

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

Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries.

Proper citation: TSDiffAna (RRID:SCR_016656) Copy   

•   Source: SciCrunch Registry

http://www.warwick.ac.uk/snpm

A toolbox for Statistical Parametric Mapping (SPM) that provides an extensible framework for voxel level non-parametric permutation/randomization tests of functional Neuroimaging experiments with independent observations. SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomization/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions. The SnPM toolbox provides an alternative to the Statistics section of SPM.

Proper citation: Statistical non-Parametric Mapping (RRID:SCR_002092) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/asltbx

Tool box for arterial spin labeled perfusion MRI data processing. It is based on SPM and Matlab. More detailed documentation can be found in asl_perf_subtract.m, the main function for calculating CBF value. It supports 3D or 4D Analyze or Nifiti format and PASL, CASL, and PCASL data. It contains the code for calculating CBF and a set of SPM batch scripts for preprocessing and statistical analysis.

Proper citation: ASL data processing tool box (RRID:SCR_005997) Copy   

•   Source: SciCrunch Registry

https://github.com/howisonlab/softcite-dataset

Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.

Proper citation: SoftCite (RRID:SCR_024411) Copy   

•   Source: SciCrunch Registry

http://hmri.info

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy   

•   Source: SciCrunch Registry

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

Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry.

Proper citation: Computational Anatomy Toolbox for SPM (RRID:SCR_019184) Copy   

•   Source: SciCrunch Registry

http://bisp.kaist.ac.kr/NIRS-SPM

A SPM and MATLAB-based software package for statistical analysis of near-infrared spectroscopy (NIRS) signals. Based on the general linear model (GLM), and Sun's tube formula / Lipschitz-Killing curvature (LKC) based expected Euler characteristics, NIRS-SPM not only provides activation maps of oxy-, deoxy-, and total-hemoglobin, but also allows for super-resolution activation localization. Additional features, including a wavelet-minimum description length detrending algorithm and cerebral metabolic rate of oxygen (CMRO2) estimation without hypercapnia, were implemented in the NIRS-SPM software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NIRS-SPM (RRID:SCR_009630) Copy   

•   Source: SciCrunch Registry

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

A free, professional viewer for SPM fMRI results. SPM (Statistical Parametric Mapping, UCL, London) is a powerful fMRI analysis software but its visualization capabilities are sometimes a limitation for the researchers. That's why Imagilys has decided to offer the neuroimaging community a free version of its commercial "BrainMagix" neuroimaging software, called "BrainMagix SPM viewer". BrainMagix SPM Viewer's Features - Professional viewer for your SPM-based fMRI activations - JAVA-programmed, cross-platform (Windows, MAC, Linux), without Matlab license, making it possible to share your results with colleagues who do not have SPM installed - Reads SPM.mat files and NIfTI images in an user-friendly way - Overlay the blobs with an atlas or any anatomical image - On the fly adjustment of threshold and cluster size - Localize your activations in an atlas - BOLD signal curves in ROIs (future feature) - Export your results as PNG images

Proper citation: BrainMagix SPM Viewer (RRID:SCR_009537) Copy   

•   Source: SciCrunch Registry

http://www.cabiatl.com/mricro/

MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyze MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms. Some features of MRIcro are: - Converts medical images to SPM friendly Analyze format. - View Analyze format images (big or little endian). - Create Analyze format headers (big or little endian). - Create 3D regions of interest (with computed volume & intensity). - Overlap multiple regions of interest. - Rotate images to match SPM template images. - Export images to BMP, JPEG, PNG or TIF format. - Yoked images: linked viewing of multiple images (e.g. view same coordinates of PET and MRI scans). Users familiar with other Windows programs will find that this software is fairly straightforward to use. Resting the mouse cursor over a button will cause a text hint to appear over the button. However, a tutorial with a step by step guide of how to use MRIcro with SPM is available.

Proper citation: MRIcro Software (RRID:SCR_008264) Copy   

•   Source: SciCrunch Registry

http://fmri.wfubmc.edu/software/Bpm

Software toolbox that performs SPM analysis with voxel-wise imaging covariates. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in Matlab with a user-friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely used T-field, has been implemented in the correlation analysis for more accurate results. Requirements: * SPM2 or SPM5 * MATLAB version 6.5 or higher

Proper citation: WFU Biological Parametric Mapping Toolbox (RRID:SCR_002613) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/tehran/

Data set of addiction studies compiled by the NeuroImaging and Analysis Group (NIAG).

Proper citation: NIAG Addiction Data (RRID:SCR_015523) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/uofm_jhu_atlas/

Probabilistic atlas of human white matter tracts/regions underlying several well-known resting state brain networks. The atlas includes group probability maps for each network, as well as each individual tract that are aligned to both the SPM and MRIStudio ICBM templates.

Proper citation: UManitoba - JHU Functionally Defined Human White Matter Atlas (RRID:SCR_015525) Copy   

•   Source: SciCrunch Registry

http://www.ucl.ac.uk/

Public research university located in London, England.

Proper citation: University College London; London; United Kingdom (RRID:SCR_011603) Copy   

•   Source: SciCrunch Registry

http://www.fz-juelich.de/ime/spm_anatomy_toolbox

A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space.

Proper citation: SPM Anatomy Toolbox (RRID:SCR_013273) Copy   

•   Source: SciCrunch Registry

https://github.com/NeuroimagingMetaAnalysis/ibma

Image-Based Meta-Analysis toolbox for SPM. Implementation of z-based statistics: Fisher's, Stouffer's.

Proper citation: IBMA toolbox (RRID:SCR_003772) Copy   

•   Source: SciCrunch Registry