HAMMER-SUITE User Manual
Contents
1. 2 3 4 Load subject data Navigate to the path of the subject data and select the subject image or multiple subject images Note that multiple images can be selected and processed together The subject image should be of the Analyze format which is also compatible with ITK Load template The template should be pre segmented into WM labeled with intensity 250 GM with intensity 150 and CSF with intensity 10 It also needs to be of the Analyze format Currently we only support the template with unsigned char 8 bit data type The sample of the template can be found as HAMMER GU I data template img Select the automatic mode Please select the automatic mode to rule out future interruption and manual interaction Click start and wait for results The whole processing time cost may vary according to different situations In general it takes 30 minutes for pre processing and 20 minutes for registration Final results as well as intermediate files share the same destination directory with the input subject data After each component in the pipeline has finished the output will be written to the output directory by appending a suffix to the original file name of the subject data The suffix indicates the component which has yielded the output The component and its corresponding suffix are listed in the following Skull Removal Cerebellum _cere Removal Suffix _conv might be applicable2. System for Qualitative and Quantitative Volumetric Analysis of Brain Images Journal of Computer Assisted Tomography vol 22 pp 827 837 1998
3. HAMMER SUITE User Manual 1 Introduction HAMMER SUITE provides a friendly environment for medical image processing It is distributed with a cranial image processing pipeline The pipeline processes raw brain MRI data through pre processing skull removal bias correction etc segmentation and registration The pipeline can be automatically executed on either a single image or multiple images Also components of the pipeline can be individually applied e g performing only segmentation to the loaded image Therefore HAMMER SUITE is quite a flexible platform for processing and analyzing brain MRI data This manual is accompanying the HAMMER SUITE release package briefing usages of the software The core of the HAMMER SUITE release is featured by the image registration function powered by the HAMMER registration algorithm 1 HAMMER Hierarchical Attribute Matching Mechanism for Elastic Registration has proven to be one of the popular brain image registration methods in the community It takes advantage of the attribute vectors in characterizing features of driving voxels in order to establish reliable correspondences between images By reducing the dissimilarity of attribute vectors in the hierarchical fashion HAMMER can acquire not only accurate but also robust registration performance The software of HAMMER SUITE is released by the IDEA Lab of the Biomedical Research Imaging Center BRIC in the University of North Carolina at Chapel Hil
4. and appended Tissue Bs due to mandatory data type cast by the pipeline Segmentation NS HAMMER i Registration ae XX can only be GM WM VN indicating _RAVENSmap_XX RAVENS maps for GM WM and ventricle respectively Tissue Density Map All outputs are in the Analyze format which are easy to interpret 4 Specification In this chapter we will elaborate the details of HAMMER SUITE If you have more questions please refer to the following FAQ or contact us directly hammer unc gmail com 4 1 Layout In general the layout of HAMMER SUITE is divided into 4 areas as in Figure 2 1 Area 1 for pipeline control 2 Area 2 for component control 3 Area 3 for data rendering 4 Area 4 for status monitoring Figure 2 Layout of HAMMER SUITE contains 4 areas typically 4 2 Pipeline All image processing tasks are arranged in a single pipeline by HAMMER SUITE Besides loading subject template data there are 5 component functions available at HAMMER SUITE currently When starting the software the default pipeline is automatically loaded providing a complete process procedure for raw brain MR data The 5 components are for skull removal cerebellum removal tissue segmentation HAMMER based registration 1 and tissue density map calculation 2 respectively Details related to each component are discussed in Section 4 3 The default pipeline can be modified to cater for different application scenarios as ea
5. ch component can be disabled by clicking the arrow right adjacent to the component button As shown in Figure 3 if the user only wants to obtain tissue segmentation results for given data the last two components can be disabled Then the pipeline will abort after successfully returning from segmentation component Load Subject Data Load Template Skull Removal Cerebellum Removal Tissue Segmentation Tissue Density Map Figure 3 The example to disable particular components in pipeline The pipeline supports both automatic and step by step modes now In the automatic mode the only thing that the user should do is to click start pipeline if the pipeline has been configured correctly The software will perform all processing steps and write outputs automatically In the step by step mode after clicking start pipeline the first component in the pipeline will be activated The user should then click apply right below the start pipeline button This will enable the current component to run until it has finished and returned Then the user should click next to activate the following component in the pipeline and apply the component once more The automatic and the step by step modes are used in different scenarios The user can use the step by step mode to determine optimal configurations and parameters for a series of data since this mode allows human interaction and review of imag
6. e processing outputs When all settings are done the user may switch to the automatic mode and process multiple datasets together In the automatic mode no human interaction is required though the user can use abort to force the program to quit 4 3 Component The pipeline is constructed by connecting individual components The order of the connected components determines the way that the input data will be processed HAMMER SUITE of current stage has 5 components skull removal cerebellum removal tissue segmentation HAMMER based registration and tissue density map calculation Users can click the button in the pipeline and access to configurations of the corresponding component e Skull removal Skull removal is usually the very first step for the raw data processing since our image segmentation and registration algorithms are designed for skull stripped images Parameter Value Bias Correction Yes e Cerebellum Removal Cerebellum removal is the step to remove cerebellum and brainstem related structures from the data in that image registration is focused on cerebrum nowadays Note that this step is not mandatory and should be complied with the template used in the pipeline If the template has no cerebellum incorporated as the template we provided cerebellum removal should be deployed to the incoming subjects Otherwise this step can be bypassed Parameter Value N3 Correction Yes Eye Orientation Left Right HAMMER I
7. l The IDEA Lab is devoted to the development of novel image analysis methods and tools as well as applications to various clinical researches and trials The developed methods include deformable registration deformable segmentation and multivariate pattern classification algorithms These methods have been applied to various studies on brain diseases and development including MCI AD Schizophrenia and Neonate Development Study heart breast cancer and prostate cancer For more details please visit the website of the lab http www med unc edu bric ideagroup 2 Installation Prior to installation please make sure that several requirements should be met on your computer e TCL TK HAMMER SUITE provides GUI powered by KWWIDGETD which needs the running environment of TCL TK Please acquire the free and open source release of TCL TK from http www tcl tk software tcltk e Perl Some scripts are written in Perl as in HAMMER SUITE Usually Linux Unix system supports Perl naturally For Windows users special attention should paid to install Perl running environment You could get it from www activestate com activeperl If you have any uncertainty please contact your system administrator for more information e Microsoft Runtime Redistributable Kit This is for Windows users only You may need to install Microsft Runtime Redistributable Kit If you have Microsoft Visual Studio available you can skip this step Now please download our la
8. low the viewers the panel allows user to determine whether two views are synchronized or whether cursors are displayed The cursor check box controls whether the cross cursor is displayed upon image renderings The yoke check box controls whether the two rendering views are synchronized Users are allowed to adjust the brightness and contrast when pressing down the right button of the mouse and move around 5 FAQ Q1 X win is forced to close when initializing the software A We have encountered this problem sometimes by using X win32 on Windows 7 However tests show that X win32 8 1 plus Windows XP do not have such a problem As the result users are encouraged to run HAMMER SUITE from the terminal on Windows XP For Windows 7 it is more stable to use Cygwin instead of the latest version of X win Q2 After installing Tcl Tk there is still an error suggesting lacking Tcl Tk files in initializing HAMMER SUITE A Please copy the two library files libtcl8 5 so and libtk8 5 so to the directory of HAMMER SUITE if encountered with this problem Users can use other versions of Tcl Tk installations besides version 8 5 6 Reference 1 D Shen and C Davatzikos HAMMER Hierarchical attribute matching mechanism for elastic registration Medical Imaging IEEE Transactions on vol 21 pp 1421 1439 2002 2 A F Goldszal C Davatzikos D L Pham M X H Yan R N Bryan and S M Resnick An Image Processing
9. teration 1 10 e Tissue Segmentation This component segments the brain into WM GM and CSF And finally we will label the WM with intensity 250 GM with intensity 150 and CSF with intensity 10 Parameter Value Artifact Removal Threshold 0 100 default 50 Artifact Removal Correction Size 0 5 default 1 Bias Correction Kernel Width 0 05 0 5 default 0 15 Bias Correction Change of CV le 2 le 4 default le 3 Bias Correction Iteration 1 100 default 50 e HAMMER Registration HAMMER SUITE provides two different versions of HAMMER registration algorithm now The first one is TPS HAMMER which generates deformation field by TPS interpolation The second one is a fast version of HAMMER which has been optimized on Intel CPUs Users are encouraged to use the fast version of HAMMER for better speed performance if they are powered with Intel CPUs Parameter Value Iteration 1 100 default 20 for TPS 50 for fast Hammer Step Ratio 0 1 default 0 05 Similarity Threshold 0 1 default 0 6 4 4 Image Rendering Two image rendering views are provided In general the loaded subject data appear in the left while the right viewer is for the template However results output by components in the pipeline can be accessed by both two views Users can use the drop down boxes on top of the viewers to navigate to the data selected By clicking l view 3 view the data can be rendered in different ways Also be
10. test releases We now have provided 3 versions for 64bit Linux Unix 32 bit Windows and 64 bit Windows respectively Please choose the proper release package to download After download please extract all files Then for Linux Unix users please add the tools subdirectory to PATH in user profile Similarly Windows users must add the win32 subdirectory to the environment variable PATH After the software has been correctly installed you are now free to start the executable binary HAMMER GUI HAMMER GUI and perform image processing tasks 3 Quick Start HAMMER SUITE provides a variety of functions to process brain MR images For raw data the default pipeline performs skull removal and cerebellum removal in pre processing Then tissue segmentation is performed to classify regions of white matter WM grey matter GM and cerebrospinal fluid CSF respectively HAMMER registration is applied and warps the subject to the space of the template After registration has finished the tissue density map Ravens map 2 related to the deformation field is calculated for convenience of subsequent analysis res oe Tissue Density Map Step by step Automatic Figure 1 Quick start requires only 4 simple steps 1 load subject data 2 load template 3 select automatic mode and then 4 click start Only 4 simple steps are needed to start a quick automatic task in HAMMER SUITE as in Figure 1 1
Download Pdf Manuals
Related Search