Brain Imaging Toolbox

| Introduction
The BIT (Brain Imaging Toolbox) is a graphical user interface to many handy programs for artifact detection/rejection, generating ROIs, and analyzing data that is in an ROI. It also contains various utility programs. There are a few programs in the toolbox that were written outside of the gablab and the URLs for those programs can be found below. The utilities are grouped into nine categories with a brief description of the groups and specific programs below. However, you can access detailed from the links within this document, or by pressing the help button near each program button in the ROI toolbox itself. If you have any questions or comments about the Toolbox's functionality or usage, please ask Sue (swg@mit.edu) or Shay (shaym@mit.edu).

| What's New

| Release Notes (04/2007)
| a new category: Connectivity Analysis, currently contains just a single utility for analysis of functional connectivity . the artifact detection tool now handles FSL motion data (.par files) as well as SPM .txt files. the artifact detection tool now lets you superimpose the task conditions on one of the graphs so you can visually check for correlations with the global mean or with the motion parameters. the global-task correlation utility was written from scratch. You can now correalte the global activation mean with the task conditions and can choose whether to collapse across different sessions or not. For more details click here .
| Release Notes (03/2007)
| new user interface that will (hopefully) make navigation between the numerous utilities more intuitive including individual help buttons for each utility. <\li> you can now launch xjview and mricro directly from the toolbox. new global and motion artifact detection tool - shows the temporal changes in both the global activation signal and motion data and enables the user to define artifacts by hand or by setting thresholds for each parameter. You can now choose to work with the temporal difference series instead of the original motion parameters values (Thanks, Dan!). new motion-task correlation analysis tool - depending on the kind of experimental design and data format, this tool may be used to display the correlation matrix between task conditions and motion parameters, with specialized tests for block design experiments. an easy to use interface for directly defining functional ROIs - based on an existing design matrix and contrasts files. After choosing the seed voxel the user may define the volume of interest and save the ROI to text files or to analyze images. a utility for applying filters (low/band/high pass) to analyze (.img) files. some minor bug fixes (timeseries, roi_deconvolve).

| Categories

| Artifacts | These tools help you find scanner artifacts or outliers in your data caused by radical head motion or scanner mishap, and repair or remove them. To read a description of how these repairs work with the SPM analysis, press here.
| Correlations | Tools for analysis of motion-task and global-task correlations.
| ROI Definitions | Tools to generate and manipulate anatomical and functional based regions of interest.
| ROI Analysis | These tools extract statistics, time course histories and measures of activation within a region of interest over an entire timecourse of images.
| Connectivity Analysis | Tools (currently a single tool) for analysis of connectivity between regions of interest.
| Display | These tools provide several different ways to visualize your region of interest in an interactive fashion or in one suitable for printing.
| Talairach Atlas | These programs allow direct use of the Talairach Atlas (instead of WFU_PickAtlas).
| General Utilities | These programs are automated tools for common user functions
| Coordinate Conversions | The tools in this section work together to allow conversions between different representation of ROIs.

| Artifacts

| Global and Motion Outliers | shows the temporal changes in both the global activation signal and motion data and enables the user to define artifacts by hand or by setting thresholds for each parameter.
| Slice Repair | Checks for outlier slices, and offers repair methods.
| Contrast Movie | Allows a user to view all the data, voxel by voxel.
| Global Variate | Old version of the artifacts detection utility. Contains some repair functionality that the new version does not, but only handles global activation outliers.
| GlmMask2 | bypasses spm_global routine that generates the mask.img and lets the user explicitly define a mask to get full brain coverage in 1st level satistics.
| Apply Filter | applies a low/band/high-pass filter to a series of analyze .img files

| Correlations

| Motion-Task Correlations | displays the correlation matrix between task conditions and motion parameters. Implements specialized tests for block design experiments.
| Global-Task Correlation | displays correlations between the global mean activation and the task conditions.

| ROI Definitions

| Anatomical ROIs | Utility to create ROI coordinate sets (.tal files) from anatomical/Brodmann landmarks.
| Functional ROIs | Creates a .tal and .img ROI file based on specified XYZ dimensions in voxels.

| ROI Analysis

| ROI stats | finds mean, min, max, and variance of data in an ROI for each image in a series. ROI is defined by a .img file.
| ROI extract | finds the mean intensity of an ROI for each user specified image. ROI is a .tal list of coordinates.
| X-Beta | a utility program to run roi_stats on multiple beta files. A good program to correlate fMRI data with behavioral data.
| Timeseries Explorer | an interactive display of timecourses from single voxels or ROIs. It also provides signal processing options and displays percent signal change for all specified conditions.
| ROI HRF Estimate | estimates the HRF responses to different conditions within an ROI.

| Connectivity Analysis

| Functional Connectivity | Utility for calculating the correlation between a source ROI and a set of target ROIs.

| Display

| Display ROIs | shows one or more ROIs in 3D interactive overlayed on a background image.
| Display Slices | shows the same thing as a montage of slices. Author: Mathew Brett. website
| Render | Improved version of the Render->Xtract Brain function, which allows user to create render*_.mat file containing any number of general 3D views of general cuts of the extracted brain. Author: Tom Sieger. website
| Studyplot | A visualization tool for meta-analyses. It enables the user to supply a database of activation points, with coordinates and other information like coordinate system, color, etc., and then have those points plotted and labeled on a variety of different brain displays.
| xjview | The xjview visualization utility. Author: Xu Cui. website
| mricro | The mricro utility for displaying and manipulating MRI images. Author: Chris Rorden. website

| Talairach Atlas

| Display_TalSpace | Displays functional clusters on Talairach atlas pages, and renders them in 3-D.
| Dump SPM to Tal | (glassbrain2.m) creates a list of points in Talairach space from a cluster region in SPM. Like Dump SPM to Anatomy, but this one returns only the Tal coordinates, suitable for input to the Talairach Daemon.
| Tal stats summary | (sum_coord.m) summarizes an output file generated by the Talairach Daemon program.

| General Utilities

| DumpSPM to Anatomy | dumps voxels from SPM Results/Volumes table, and names all the points. Allows the user to identify anatomy locations of active SPM cluster regions.
| Find anatomy names | finds names (hemisphere, lobe, Brodmann area) for one or more [XYZ] points in MNI space using the WFU_PickAtlas database.
| Modify Pathnames | When files are moved or old files are restored, the names embedded in SPM.mat are not valid. This program (modifySPM2.m) can repair the file names.
| Contrast Copier | collects contrast images from different subjects and puts them in a single folder. A convenient program for 2nd analyses, eg to correlate fMRI data with behavioral data.
| Create Head Mask | automatically generates a reasonable full-head mask. Designed to eliminate the wrap-around artifact in spiral scan data.

| Coordinate Conversions

An ROI can be expressed as: An image of 1's and 0's. ( .img file ) A list of points in MNI space ( .txt file ) in mm units. A list of points in Talaraich space ( .tal file ) in mm units. A list of points in single subject space. The tools in this section work together to allow conversions between these spaces.
| img2txt | converts an ROI img ( in MNI space ) into list of points (.txt file.)
| mni2tal | converts a list of points in MNI space to a list in Talaraich space (.tal file). Uses Mathew Brett's conversion.
| txt2img | converts a list of points in MNI space into a .img file. Program asks for a sample image in order to set the voxel size and image dimensions.
| tal2mni | converts a list of points in Talaraich space to a list in MNI space. It appends _mni to the filename in its translation process. Uses Mathew Brett's conversion.
| MNI to Subject | converts a list of points in MNI space to a list of points in single subject space by performing a reverse noramlization with the (_sn.mat) calculated by SPM.