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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
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
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
http://www.nitrc.org/projects/clinicaltbx/
A clinical toolbox useful for normalizing data from individuals with brain injury and/or modalities popular in the clinical environment (CT). It supports either enantiomorphic or lesion-masked normalization. It can be either scripted or used with SPM's simple graphical interface.
Proper citation: Clinical Toolbox for SPM (RRID:SCR_014096) Copy
https://www.nitrc.org/projects/imcalc/
A collection of functions with batch functionality for SPM: * user entered expression (one set of volumes); * binarize non-zero voxels; * binarize/threshold each image; * binarize non-zero voxels, sum, rebinarize; * voxelwise calculations on pairs (add sub mult div ... etc.); * flip sign of all non-zero voxels; * x-flip image along y = 0; * mask images to a template; * T-to-Z transform; * Winsorize (cap) extreme values; * Z-score transform of image relative to its global mean and SD; * write single voxels to a .nii; * create a cluster image; * split cluster image into constituent images; * write hemisphere masks from template; * homotopic calculations; * replace zeros with __; * pad image with extra voxels;
Proper citation: imcalc: SPM batch image calculator (RRID:SCR_000868) Copy
http://cibsr.stanford.edu/tools/human-brain-project/artrepair-software.html
A toolbox for SPM to improve fMRI analysis of high motion pediatric and clinical subjects. The toolbox includes special algorithms for motion adjustment, data repair, and noise filtering, and methods to find outlier subjects in group studies. Visualization tools are included for quality checking the data, including a movie format for viewing all data and all contrast estimates on every voxel of every subject. Methods are included to quantify results into percent signal change. * Operating System: OS Independent * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 * execution requires: SPM
Proper citation: ArtRepair for robust fMRI (RRID:SCR_005990) Copy
http://marsbar.sourceforge.net/
A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.
Proper citation: MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) Copy
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