Anatomical Automatic Labeling Manual

Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. Tzourio-Mazoyer N(1). Regions of interest were then drawn manually with the same software every 2 mm on the axial slices of the high-resolution MNI single subject. The 90 AVOI were. Manual lymphatic drainage in the horse for. The development of this manual lymphatic treatment concept is based mainly on the anatomical studies. Anatomical Automatic Labeling Manual Muscle Grades Containers may be included in the Reference Listing of Accepted Construction Materials.

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 between,, and. The distinction between Toolboxes and Utilities can be blurry, but for the purposes of this page we define a toolbox to be a utility that can be completely operated via a graphical user interface.

If you notice inaccuracies or out of date links, please email the. Likewise, to have your SPM extension linked here, send an including a URL, a contact email, and a brief summary (please note if any MATLAB toolboxes are required, or if it is platform-specific). The SPM Developers take no responsibility for the usability of the extensions listed here.

In particular, some extensions may be mutually incompatible. Please contact the respective extension authors with questions and problems (though CC'ing answered questions to the will be appreciated). Extensions compatible with SPM12, SPM8, SPM5, SPM2, SPM99. The list of SPM extensions is also available as an. Note: All email addresses in this page have their '@' replaced with '_at_' to minimize spam. Please reverse this change before emailing.

Quick Links: : : : Toolboxes. ALI - Automated Lesion Identification SPM12 SPM8 SPM5 Summary: ALI is a research tool for lesion delineation and spatial normalization for patients with brain damage.

It uses the unified normalisation-segmentation algorithm with an explicit extra prior for the lesion that is refined iteratively in a patient-specific manner. Lesions are then defined as a set of outlier voxels while taking into account the typical variability in anatomy in healthy controls. ALI can also generate lesion overlap maps.

BRANT (BRAinNetome fMRI Toolkit) SPM12 SPM8 Summary: BRANT (BRAinNetome fMRI Toolkit) is a MATLAB based toolbox which includes batch scripts with automatically generated GUIs for the preprocessing pipeline, brain spontaneous activity, functional connectivity analysis, complex network analysis, statistical analysis and results visualization. A universal input/output interface was designed for most functions, and users can customize their own scripts into GUIs by adding a few lines of MATLAB code. We've also implemented efficient file loading/saving functions and parallel computing scripts using matrix operations, OPENCL and multithreading to speed up data processing. BredeQuery SPM5 Summary: BredeQuery plugin for SPM5 - enables coordinate-based meta-analytic search of related literature for brain regions directly from SPM5 environment.

The coordinate-based search is performed using Finn Aarup Nielsen's Brede Database. Works with coordinates in Talairach and MNI space, MNI-to-Talairach transformations are available (Brett and Lancaster transformations).

Moreover, query results can be exported automatically to the suitable bibliographic file format (BibTeX, Reference Manager, RefWorks, EndNote). Bspmview SPM12 SPM8 Summary: Another SPM viewing program.

Intuitive and customizable user interface for exploring statistical images (e.g., spmT*), including display of positive and/or negative effects; voxel- and cluster-level thresholding; instant anatomical labeling; and customizable color maps. Easily generate customizable surface renderings. Save thresholded whole-brain maps, specific clusters, and ROIs.

View results tables interactively, and save publication-ready tables. Although built for viewing statistical images, it allows viewing other image types (e.g., contrast/mask/ROI images). DPARSF- Data Processing Assistant for Resting-State fMRI SPM8 SPM5 Summary: DPARSF is a convenient plug-in software based on SPM and REST. You just need to arrange your DICOM files, and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data, FC, ReHo, ALFF and fALFF results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. You can use DPARSF to extract AAL or ROI time courses (or extract Gray Matter Volume of AAL regions, command line only) efficiently if you want to perform small-world analysis.

DPARSF basic edition is very easy to use, just click on buttons if you are not sure what it means, popup tips would tell you what you need to do. DPARSF advanced edition is much more flexible, you can use it to reorient your images interactively or define regions of interest interactively. You can skip or combine the processing steps in DPARSF advanced edition freely. FECM - Fast eigenvector centrality mapping SPM12 SPM8 SPM5 Summary: This toolbox computes eigenvector centrality maps from 4D fMRI data sets in the NIfTI format -- both.nii and.nii.gz extensions are supported. It uses the fast ECM algorithm, sidestepping the need to compute the whole voxel-to-voxel connectivity matrix. The easiest way to control the algorithm is by calling the 'fegui' function which brings up a menu where fMRI data, masks and atlases can be selected.

Casio Keyboard Rhythms Download on this page. 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). GPPI SPM8 Summary: An automated toolbox for a generalized form of psychophysiological interactions for SPM and FSFAST. The generalized form of context-dependent PPI approach ('cond' option) has increased flexibility of statistical modeling, and potentially improves model fit, specificity to true negative findings, and sensitivity to true positive findings. When using the toolbox, please cite 'A Generalized Form of Context-Dependent Psychophysiological Interactions (gPPI): A Comparison to Standard Approaches', McLaren et al. NeuroImage 2012.

GridCAT - Grid Code Analysis Toolbox SPM12 Summary: The GridCAT allows users to carry out automated analysis of human grid cell codes in fMRI data. The GridCAT performs all analyses, from estimation and fitting of the grid code in the general linear model, to the generation of grid code metrics and plots. It provides a graphical user interface for researchers less comfortable with programming; researchers confident with programming, however, can edit the open-source code accompanying the GridCAT to implement their own analysis pipelines. An example dataset is provided together with a detailed manual, so that users can explore the GridCAT's functionality. Grocer SPM8 SPM5 Summary: This toolbox contains many kinds of kits that you may be interested in for CBF(Cerebral Blood Flow) data analysis. This toolbox is run and tested on SPM8 with MATLAB 7.6.0 (R2008a) under Linux. Theoretically, most of the functions (except the first two menus which are specially designed for the Batch Editor of SPM8) of this toolbox should be compatible with SPM5 and should also work smoothly under the Windows OS.

Read the manual in the package for more details. IBASPM (Individual Brain Atlases using SPM) SPM5 SPM2 Summary: A toolbox with GUI for segmenting automatically cerebral structures in MRI images in the individual anatomy space. Through this set of routines is able to compute the volume of gross anatomical structures. Other facilities are related to the computation of the SPAMs (Statistical Probability Anatomy Maps) and MaxPro (Maximum probability) maps that can be used in classification procedures. Also the computation of the gray matter, white matter, cerebral spinal fluid (CSF) volumes by hemisphere and total brain volume is affordable through this toolbox. All programs have been developed in the Neuroimaging Department, Cuban Neuroscience Center.

IBrain analysis toolbox SPM8 SPM5 SPM2 Summary: The iBrain analysis toolbox for SPM is a free toolbox that provides an automated processing pipeline for various single- or multi-subject and/or multi-session functional neuroimaging experiments. The pipeline includes image conversion from scanner-specific formats, pre-processing, statistical analysis, region-of-interest analysis, and display. It is possible to specify a complete analysis stream in advance (i.e. Before any processing is actually performed).

Analysis paradigms supported include block-design, event-related, simultaneous EEG/fMRI, and functional connectivity. IBrain Laterality Toolbox SPM8 SPM5 SPM2 Summary: The iBrain Laterality Toolbox contains MATLAB scripts that implement an objective threshold-independent assessment of whether the balance of activity between two regions of interest is typical or atypical, based on statistical comparison between an individual and a group of controls. The toolbox displays laterality index (LI) plots as a function of an adaptive threshold, and provides statistical assessment of the plots to determine lateralisation. Lesion_gnb Toolbox SPM12 Summary: The toolbox is designed for automatically classifying voxels that correspond to chronic stroke lesions in T1-weighted MRI scans. It utilizes the SPM12 New Segment and Normalization routines to obtain template-normalized patient tissue probabilistic maps (TPMs) from T1-weighted scans.

These TPMs are used along with the prior probability maps (PPMs) to construct feature maps encoding information about which voxels are likely to correspond to missing and abnormal tissue. The feature maps are input as predictors to a fully trained and cross-validated Gaussian Naive Bayes classifier to obtain predictions about which voxels correspond to lesioned tissue.

Simple post-processing (smoothing and cluster thresholding) can be applied to reduce the occurrence of false positives. No control group is necessary for lesion. The toolbox includes the option for obtaining and post-processing individual patient lesion predictions entirely via a simple dialogue-based interface, and also includes examples scripts for running batch jobs. MARS - Morphologically and Anatomically accuRate Segmentation SPM8 Summary: MARS is an extended toolbox for SPM software. It is developed based on the SPM8 toolbox 'New Segment'. MARS added the morphological constraints on neighboring tissue voxels encoded by Markov Random Field (MRF).

This MRF information is added into the updating equation of the E-step of the algorithm, not just as a post-processing step. Compared to the New Segment, the resulting segmentation is shown to be more smooth and with less discontinuities, while at the same time the accuracy is not significantly changed.

Multifocal - Create multifocal fMRI designs SPM2 Summary: Multifocal fMRI designs allows simultaneous measurement of local signals in the cortex from multiple visual field regions in parallel. This toolbox creates multifocal fMRI stimuli for Presentation(TM), accounting for the spatial and temporal design, size of the stimulus (M-scaling), contrast, and position in the display. Also contains a separate script to estimate the data with SPM2. Tested with matlab 7.3 running in Fedora Core 6 linux.

MRTOOL - Toolbox for structural MR imaging analyses SPM12 Summary: In view of the increasing availability of MR imaging data for clinical investigations, we introduce MRTool, a comprehensive collection of analysis tools in the form of a SPM12 plugin toolbox. At the current stage, it consists of four modules. (1) 'T1-w/T2-w image' for the generation of the multimodal ratio image. (2) 'Optimized Bias Correction parameters' for the definition of the optimal set of input parameters (regularization and FWHM) required during the bias correction of MR images in SPM12. (3) 'Brain Extraction' for the generation of skull-stripped images.

(4) 'Optimized Normalization' for an enhanced spatial registration and segmentation of elderly subjects characterized by a marked ventricular enlargement and advanced atrophy. PETPVE12 - Partial Volume Effects correction of PET images SPM12 Summary: This toolbox implements two popular algorithms for partial volume correction (PVC) of PET images within an easy to use GUI-based pipeline that provides high transparency and flexibility with respect to the implemented routines, processing choices and parameter settings for the distinct PVC methods. The implemented algorithms include the 'Muller-Gartner' method for 3-compartmental voxel-wise PVC, and the 'Geometric Transfer Matrix/Rousset' method for region-wise PVC. Some of the toolbox routines require Matlab's Image Processing Toolbox. TAPAS PhysIO Toolbox SPM12 SPM8 Summary: This toolbox provides model-based physiological noise correction of fMRI data using peripheral measures of respiration and cardiac pulsation. It incorporates noise models of cardiac/respiratory phase (RETROICOR, Glover et al. 2000), as well as heart rate variability and respiratory volume per time (cardiac response function, Chang et.

Al, 2009, respiratory response function, Birn et al. The toolbox is usable via the SPM batch editor, performs automatic pre-processing of noisy peripheral data and outputs nuisance regressor files directly suitable for SPM ('multiple_regressors.txt'). SAfE - Straightforward Analysis of fMRI and EEG-fMRI SPM8 Summary: Straightforward analysis of fMRI experiments, from the preprocessing until the statistical maps, with little user input. Especially suited for situations when the number of conditions and timing of the events vary among subjects, such as in EEG-fMRI analysis. When the onset and duration of the events are obtained from the EEG, a VBA macro in Microsoft Excel reads the EEG markers file and creates the appropriate spreadsheet. GUI and batch processing. SPM EEG Spike detection toolbox SPM12 Summary: SpikeDet is a fully automated method of interictal spike detection in an EEG record that adapts to interpatient and intrapatient variation in spike morphology.

The algorithm works in five steps. (1) Spikes are detected using parameters suitable for highly sensitive detection. (2) Detected spikes are separated into clusters. (3) The number of clusters is automatically adjusted. (4) Centroids are used as templates for more specific spike detections, therefore adapting to the types of spike morphology.

(5) Detected spikes are summed. SwE - Sandwich Estimator Toolbox for Longitudinal & Repeated Measures Data SPM12 SPM8 Summary: SwE is a toolbox to accommodate general repeated measures and longitudinal data. It makes no assumption about balanced designs and, through the use of a 'marginal model', allows either between- or within-subject variables (e. Sam Sparro Return To Paradise Rar. g.

In one longitudinal design, you can model both time and gender). Variance (& covariance) are estimated separately for each group. It has accurate parametric results that work reasonably well for at least 20 subjects per group, and otherwise a bootstrap resampling inference procedure (that additional provides FWE voxel- or cluster-wise inferences). UF2C - User Friendly Functional Connectivity SPM12 SPM8 Summary: UF2C aims to simplify and organize functional connectivity studies in neuroimaging through a clean and validated methodology, without sacrificing quality.

UF2C has a full processing pipeline: The user only needs to select the raw functional and structural NIfTI files from the subjects. The graphical user interface makes the processing and analysis options accessible for neuroscientists, with reasonable choices of default settings. UF2C allows the user to study functional connectivity both through a quantitative view that provides detailed values of average connectivity, and through a spatial view that provides statistical maps that can be directly used for further analyses. All results are carefully organized in distinct folders for each subject, and a common folder is generated with a log file reporting the quantitative results of all the analyzed subjects. VDB SPM12 SPM8 Summary: The software package VDB 1.0 has been designed for analysis neural activities of brain regions evoked by the virtual stimulating signal (or the virtual task signal). In addition, this tool can also help researchers to study causal relationships among brain regions.

Current version of this software package is VDB1. The current release is designed for the analysis of resting-sate fMRI. VDB 1.0 software package had been tested in Windows 7/Windows 10(32 and 64 bit) platforms. This software uses the 4D NIFTI-1 file format for the image data. All images must be written as 4D NIFTI-1.

All data must be preprocessed by using SPM before these data can be processed utilizing the software package VDB1. WFU_PickAtlas SPM12 SPM8 SPM5 SPM2 SPM99 Summary: This software provides a method for generating ROI masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label and Tissue Type.

The atlases have been extended to the vertex in MNI space (see Atlas Modifications under Technical Notes). Additional atlases can be added without much difficulty. The toolbox was developed in the Functional MRI Laboratory at the Wake Forest University School of Medicine.

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 2. The function for quantifying cerebral blood flow should be SPM independent except the image reading and writing functions from SPM. In our website, you can find example ASL data acquired using PASL, CASL, or pseudo-CASL sequence. Customized scripts have been provided for each example dataset.

Questions regarding ASL data processing or general ASL MRI can be posted in Author: URL. BrainMagix SPM Viewer SPM8 SPM5 Summary: A free, professional viewer for SPM fMRI activations. JAVA-programmed, cross-platform (Windows, MAC, Linux), without Matlab license, making it possible to share your results with colleagues who do not have SPM installed. Read SPM.mat files and NIfTI images in an user-friendly way. Overlay the blobs with an atlas or any anatomical image. On the fly adjustment of threshold and cluster size. Localize your activations in an atlas.

BOLD signal curves in ROIs. Export results as PNG images. MatlabTFCE - Standalone MATLAB implementation of permutation TFCE correction Summary: This package offers a standalone implementation of multiple comparison correction for fMRI data.

It achieves this through a permutation testing approach which controls familywise error rate by comparing voxelwise statistics to the maximal statistics obtained from repeating the analysis with randomized data. This maximal permuted statistic correction technique is combined with the threshold free cluster enhancement (TFCE) transformation due to Smith & Nichols (2009), which obviates the need for arbitrary voxelwise cluster-forming thresholds and instead produces continuous correct p-values for all voxels.