WFU Pickatlas
v 3.0.5
maldjian@wfubmc.edu
WFU PickAtlas User Manual v3.0
ANSIR Laboratory
Wake Forest University School of Medicine
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WFU Pickatlas
v 3.0.5
maldjian@wfubmc.edu
WFU PickAtlas version 3.0 User Manual
Joseph Maldjian, MD
1. SOFTWARE DESCRIPTION, INSTALLATION AND SETUP 1.1 DESCRIPTION
1.2 HARDWARE AND SOFTWARE REQUIREMENTS 1.3 PROGRAM INSTALLATION
1.4 REFERENCING THE SOFTWARE 2. USING THE WFU_PICKATLAS 2.1 GUI LAYOUT
2.2 GENERATING MASKS USING THE PICKATLAS TOOL 2.3 GENERATING A MASK IN BASIC MODE
2.4 GENERATING A MASK IN ADVANCED MODE 2.5 COORDINATE CONVERTER 2.5 COORDINATE CONVERTER 2.6 MASK DILATION 2.7 SHAPE DEFINITION 2.8 TABLE GENERATION 2.9 COMMAND LINE USE 3 ROI ANALYSIS 3.1 PERFORMING ATLAS-BASED ROI ANALYSES IN SPM: 3.2 SELECTING A SAVED MASK FILE
3.3 SELECTING AN ROI USING THE PICKATLAS 4 USING RESULTS VIEWER 4.1 STARTING THE RESULTS VIEWER 4.2 THE RESULTS VIEWER INTERFACE 4.3 THE SAMPLE DATASET 4.4 SPM DATASET 4.5 FSL DATASET 4.6 AFNI DATASET 5. TECHNICAL NOTES 5.1 INTEGRATION WITH SPM 5.2 ATLAS MODIFICATIONS 5.3 ACCESSING THE ATLASES REFERENCES 3 3 3 3 4 5 5 5 6 7 7 8 8 9 10 10 11 11 11 11 12 12 12 14 14 14 16 18 18 19 19 19
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WFU Pickatlas
v 3.0.5
maldjian@wfubmc.edu
1. Software Description, Installation and Setup
1.1 Description
The PickAtlas software toolboxes [1, 2] provide methods for generating ROI masks based on the Talairach Daemon (TD) database [3, 4] as well as other human and non-human animal atlases, and exploring analysis results. The TD atlases include Brodmann area, Lobar,
Hemisphere, Anatomic Label (gyral anatomy) and Tissue Type. The atlases have been extended to the vertex in MNI space (see Atlas Modifications under Technical Notes). Other atlases included in this release are the AAL atlas, ICBM label atlas, the UNC primate Brain Atlas
(rhesus), the Virginia Tech/Wake Forest Vervet atlas, and the Brookhaven National Laboratory Mouse Atlas. Additional atlases can be added without much difficulty (see Developer’s
manual). The toolbox was developed in the ANSIR Laboratory at the Wake Forest University School of Medicine. Questions can be referred to maldjian@wfubmc.edu .
1.2 Hardware and Software Requirements
Matlab
The wfu_pickatlas toolboxes require at least Matlab 2008a. SPM
The wfu_pickatlas and wfu_results toolboxes can run outside of SPM. All toolboxes are compatible with SPM8 (from the Wellcome Trust Centre for Neuroimaging, London, UK). Linux
The toolbox has been evaluated on Linux platforms. Windows
It has not been extensively evaluated for Windows. The minimum screen resolution must be 1280x1024 or all the buttons will not appear.
1.3 Program Installation
The WFU_PickAtlas toolbox can be obtained at www.ansir.wfubmc.edu .
Uncompress and untar the the gz file in a temporary location.
Copy the wfu_pickatlas, wfu_results, and wfu_tbx_common directories to the toolbox directory of your SPM installation.
If you are using WINZIP to extract the tar file version of the distribution, you must turn off the “Tar file smart CR/LF conversion option” (found under Options, Configuration,
Miscellaneous, Other). If this option is not turned off, the wfu_pickatlas.fig will be corrupted and the program will not start.
This will create several subdirectories called wfu_pickatlas, wfu_results, and
wfu_tbx_common in your SPM toolbox directory. When run from the SPM Toolboxes pull-down menu, the appropriate toolbox path will be automatically prepended to the current Matlab path.
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WFU Pickatlas
v 3.0.5
maldjian@wfubmc.edu
To run from the command line without first accessing the program from the SPM Toolboxes pull-down list, you will need to set your Matlab path to directly access the wfu_pickatlas directory:
Adding the WFU_PickAtlas toolboxes to the path
addpath(SPMpath/toolbox/wfu_pickatlas);
If the software is installed properly, you should be able to call up the graphical user interface (GUI) from the Matlab command prompt with:
Lauching the PickAtlas from the Matlab command prompt
wfu_pickatlas;
1.4 Referencing the software
When using this tool for a paper please reference [1, 2]:
Maldjian, JA, Laurienti, PJ, Burdette, JB, Kraft RA. An Automated Method for Neuroanatomic and Cytoarchitectonic Atlas-based Interrogation of fMRI Data Sets. NeuroImage 2003. 19:1233-1239.
Maldjian JA, Laurienti PJ, Burdette JH. Precentral Gyrus Discrepancy in Electronic Versions of the Talairach Atlas. Neuroimage 2004; 21(1) 450-455.
The above manuscripts provide a complete description of how the atlas volumes were
generated and validated. If using any of the Talairach Daemon database atlases, please reference [3, 4]:
Lancaster JL, Summerln JL, Rainey L, Freitas CS, Fox PT. The Talairach Daemon, a database server for Talairach Atlas Labels. NeuroImage 1997;5:S633
Lancaster JL, Woldorff MG, Parsons LM, et al. Automated Talairach atlas labels for functional brain mapping. Hum Brain Mapp 2000;10:120-131
If using the included aal atlas, please also reference [5]:
Tzourio-Mazoyer N, Landeau B, Papathanassiou D, Crivello F, Etard O, Delcroix N, Mazoyer B, Joliot M. Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. Neuroimage. 2002; 15(1):273-89.
For other atlases please reference the sources cited in the pickatlas GUI using the “atlas information” button at the bottom of the left atlas selection pane.
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WFU Pickatlas
v 3.0.5
maldjian@wfubmc.edu
2. Using the WFU_PickAtlas
2.1 GUI layout
The PickAtlas tool is divided into 3 primary columns (Figure 1). The left most column includes the atlases that can be used to generate a mask. The right most column is the working region that lists the areas to be included in the mask. The center column includes
function buttons and an anatomic image with the selected mask overlaid. The lower most portion of the tool includes coordinate conversions and Talairach Daemon labels for any point that is chosen on the anatomic image as
described below. The title bar of the left window reports the atlas in use. By double clicking on one of the atlases (i.e,. Brodmann area+), the corresponding subregions are listed and the title bar updates to display that the Brodmann Area
Figure 1. PickAtlas GUI. The left most pane lists the atlas types atlas is selected. Double clicking
and is used for navigating the atlas subregions. The right most on any of the subregions moves it
pane lists the selected regions. to the working regions pane
(right). In Basic mode, anything in
the working region pane is automatically added to the mask and all operations are considered unions. In Advanced mode (see Figure 6), unions, intersections, and multiple combinations of regions are allowed. In advanced mode, the commit button must be pressed (appears under the working region pane) before an ROI is added to the final mask. Both Basic and Advanced mode allow the use of the dilation operator. The default operation is for a mask to be written with a single value for the masked region (a value of 1). The “Write Independent Regions” selector assigns a unique value to each region in the mask (up to 255).
The bottom of the GUI contains a coordinate converter for converting between display, MNI, and Talairach coordinate systems. Clicking on any point in the displayed image updates the coordinate values. Similarly, a point can be entered for any coordinate system and set using the corresponding GO button.
2.2 Generating masks using the PickAtlas Tool
The PickAtlas tool has basic (default) and advanced modes. The mode is set by choosing “basic” or “advanced” in the top middle column. In basic mode all areas are combined into a single union. In addition, any dilations (see section 2.8 Mask Dilation) are applied to all selected
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