Brain Imaging Toolbox

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.