Functional Imaging BIRN Releases

SPM XML Toolbox Ver 1.1

dbkeator@stage.nitrcce.org (David Keator) — Wed, 26 Oct 2011 18:33:00 GMT

This is essentially the same release as ver 1.0 but with support for Matlab 7.6.x. There were some matlab functions that changed and/or became depricated. A version 2.0 will be forthcoming that supports SPM8 and XCEDE 2.0 schemas.

Clinical Assessment Layout Mgr 2.2

dbkeator@stage.nitrcce.org (David Keator) — Wed, 10 Nov 2010 18:19:00 GMT

Description:

This application facilitates preparation on online clinical assessment entry forms for the HID database application. Each online clinical assessment consists of multiple pages. Each page consists of an arbitary depth container and display elements hierarchy. A container contains zero or more display components. A display component corresponds to a form field like text entry field, radio button or to styled text. Each container has a layout manager which constraints how its children (other containers and/or display elements) are laid out with respect to each other and their parent container.

The management of clinical data within the HID is handled by the Clinical Assessment Layout Manager (CALM) and associated Generic Assessment Management Engine (GAME). The main purpose of CALM is to streamline the development of online forms for data entry and for the maintenance of an ever-growing number of clinical assessments. It is composed of an off-line multipage form layout editor and code generator. Online data entry and management is the responsibility of the GAME web application.

Once the form(s) of a clinical assessment are laid out spatially using CALM, the form input fields are linked with the assessment information from the database. The form editor then renders the form using XForms technology (designed to meet the shortcomings of HTML forms, by including device independence, strong separation of purpose from presentation, and universal accessibility). The code generator section of the form editor uses plug-ins to generate document/code for different user interface platforms. The XSL stylesheet generates a Java Server Pages (JSP) document for each form in the clinical assessment. The plug-in also generates a Struts Form Bean for the clinical assessment. Using the JSPs and Form Bean(s) generated by the form editor, GAME provides the data maintenance logic for adding and editing any clinical assessment. Eighteen clinical assessments to date have been created and deployed using this method.

Human Imaging Database (HID) 2.2

dbkeator@stage.nitrcce.org (David Keator) — Wed, 10 Nov 2010 18:06:00 GMT

Release 2.2 of the Human Imaging Database web interface (clinical directory) and database schema (schema directory).

Notes:
The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large.

The HID system is comprised of the HID Schema (in Oracle and PostgreSQL), the HID Graphical User Interface enabling the navigation through the HID and experimental hierarchies, and lastly the Clinical Assessment Layout Manager (CALM) coupled with General Assessment Manager Engine to manage and integrate clinical data. All components of the HID system can be found by clicking the Download link.

The complete system is used to manage and query local data at various research sites within BIRN. In addition to local operations, the system allows for mediated queries across multiple federated databases allowing researchers to discover data across all relevant sites. The current system provides an intuitive and easy to use clinical and/or derived data complex query builder, query result export for statistical analysis tools, statistical analysis of query results through the BIRN Portal, MRI image preview, conversion and download of the imaging data, as well as integration with BIRN Portal tools for data management and manipulation. Additionally, the system is being developed to provide a complete data management solution where all information regarding a subject can be maintained. A majority of the source code is generated from the database schema itself, allowing changes of the database schema to be reflected in the system easily. Development of the system continues to be a coordinated and parallel effort across multiple BIRN sites. The deployed architecture provides the extensibility, maintainability, security and parallel development features as demanded by the participating BIRN sites for building, accessing and maintaining their human brain imaging and related clinical data.

This latest release contains many new features including the administration console, support for GridFTP, derived data uploads via XCEDE XML, remote tabletPC enabled clinical assessment uploads.

XCEDE XML-Based Clinical Experiment Data Exchange Schema (XCEDE) 2.0

dyounes@stage.nitrcce.org (Danny Younes) — Mon, 16 Jun 2008 23:47:00 GMT

The XCEDE schema provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes information into five general hierarchical levels:
•a complete project
•studies within a project
•subjects involved in the studies
•visits for each of the subjects
•the full description of the subject's participation during each visit

Each of these sub-schemas is composed of information relevant to that aspect of an experiment and can be stored in separate XML files or spliced into one large file allowing for the XML data to be stored in a hierarchical directory structure along with the primary data. Each sub-schema also allows for the storage of data provenance information allowing for a traceable record of processing and/or changes to the underlying data. Additionally, the sub-schemas contain support for derived statistical data in the form of human imaging activation maps and simple statistical value lists.
XCEDE was originally designed in the context of neuroimaging studies and complements the Biomedical Informatics Research Network (BIRN) Human Imaging Database, an extensible database and intuitive web-based user interface for the management, discovery, retrieval, and analysis of clinical and brain imaging data. This close coupling allows for an interchangeable source-sink relationship between the database and the XML files, which can be used for the import/export of data to/from the database, the standardized transport and interchange of experimental data, the local storage of experimental information within data collections, and human and machine readable description of the actual data.
The core XCEDE schema supports several major extensible components:
•A flexible experimental hierarchy: As illustrated in the above, the XCEDE experiment hierarchy consists of several levels (project, subject, visit, study, episode and acquisition) representing divisions of experiment data at various granularities. Elements at each level contain level-specific "info" elements, whose schema types may be derived to store experiment-specific or data modality-specific metadata. The linking mechanism between levels is flexible enough to support the omission of levels if the schema user finds them unnecessary.
•Experimental protocols: Specifications for order, number and time of experimental components (e.g. assessments within a clinical interview, scans within a scanning session, visits within a project) are supported using a generic protocol element.
•Event data: XCEDE has elements to support time-interval-annotated metadata such as behavioral stimulus/response data, per-timepoint QA metrics, etc.
•Data provenance: The complete history of a processing stream can be stored and propagated using provenance elements provided by the XCEDE schema.
•Plus: application-specific file and analysis lists (catalogs), interfaces to binary data, arbitrary user and application annotations, derived data, and more.

Stability Phantom QA Procedure Function BIRN Stability Phantom QA Procedures 2.0

gadde@stage.nitrcce.org (Syam Gadde) — Tue, 28 Jul 2009 15:02:00 GMT

The tool fmriqa_phantomqa.pl implements several recommendations of the fBIRN Calibration working group in analyzing fMRI data from a spherical agar-filled phantom. This version of the recommendations were implemented in the fBIRN starting in 2007, and have been enhanced and extended to the current date (2009). A major subset of these recommendations come from the following publication:

Friedman, L., Glover, G., "Report on a Multicenter fMRI Quality Assurance Protocol", J Magn Reson Imaging. June 2006. 23(6):827-39.

The QA tools are available in "BXH/XCEDE Tools":

http://www.nitrc.org/projects/bxh_xcede_tools

Documentation for the QA tools are available here:

https://xwiki.nbirn.org:8443/xwiki/bin/view/Function-BIRN/AutomatedQA

SPM XML Toolbox SPM XML Toolbox Manual

dyounes@stage.nitrcce.org (Danny Younes) — Tue, 21 Jul 2009 20:14:00 GMT

A toolbox for SPM was created to capture the results from activation maps using the XML activation schema. The toolbox supports both SPM99 and SPM2 statistical structures and has been tested on SUN, LINUX, and Microsoft Windows operating systems. The toolbox has been used to capture PET and fMRI analysis results and the associated analysis model specifications.

Support for anatomical labeling is provided via the Talairach Daemon and Automated Anatomical Labeling toolkits. Anatomical labeling is only available if the Talairach and/or AAL toolboxes are installed on the system.

Optional MNI space to Talairach space corrections are supported via Matthew Brett’s mni2tal scripts. Additional atlas support will be added as those atlases become available and can be integrated into the SPM/matlab environment.

The results are classified into project, study, subject, visit, or series level statistics. By classifying the results under a specific level, additional meta-data can be stored with the statistical results. For instance, one may want to store the statistical activations of a project level analysis across multiple subjects with the description of the protocols used in that project. Support for this type of extended meta-data is provided in the XML-based Clinical Experiment Data Exchange schema (XCEDE).

The toolbox supports independent, user selectable storage and labeling of set, cluster, and voxel level statistics. The storage of x,y, and z coordinates of significant clusters and/or voxels can be specified. The toolbox also provides a user definable description field allowing for custom annotation of the statistical output

Installation:

To install the toolbox,
1. download the TAR file and uncompress it in your SPM_ROOT/toolbox directory.
2. Restart SPM
3. Now you should see "XML_Toolbox" as a selection in the "Toolboxes" drop down menu within SPM's user interface

References:

Keator D, Gadde S, Grethe J, Taylor D, Potkin S, FIRST BIRN (2005 submitted) A General XML Schema and Associated SPM Toolbox for Storage and Retrieval of Neuro-Imaging Results and Anatomical Labels.

SPM XML Toolbox SPM XML Toolbox

dyounes@stage.nitrcce.org (Danny Younes) — Tue, 21 Jul 2009 20:11:00 GMT

A toolbox for SPM was created to capture the results from activation maps using the XML activation schema. The toolbox supports both SPM99 and SPM2 statistical structures and has been tested on SUN, LINUX, and Microsoft Windows operating systems. The toolbox has been used to capture PET and fMRI analysis results and the associated analysis model specifications.

Support for anatomical labeling is provided via the Talairach Daemon and Automated Anatomical Labeling toolkits. Anatomical labeling is only available if the Talairach and/or AAL toolboxes are installed on the system.

Optional MNI space to Talairach space corrections are supported via Matthew Brett’s mni2tal scripts. Additional atlas support will be added as those atlases become available and can be integrated into the SPM/matlab environment.

The results are classified into project, study, subject, visit, or series level statistics. By classifying the results under a specific level, additional meta-data can be stored with the statistical results. For instance, one may want to store the statistical activations of a project level analysis across multiple subjects with the description of the protocols used in that project. Support for this type of extended meta-data is provided in the XML-based Clinical Experiment Data Exchange schema (XCEDE).

The toolbox supports independent, user selectable storage and labeling of set, cluster, and voxel level statistics. The storage of x,y, and z coordinates of significant clusters and/or voxels can be specified. The toolbox also provides a user definable description field allowing for custom annotation of the statistical output.

To install the toolbox,
1. download the TAR file and uncompress it in your SPM_ROOT/toolbox directory.
2. Restart SPM
3. Now you should see "XML_Toolbox" as a selection in the "Toolboxes" drop down menu within SPM's user interface

References:

Keator D, Gadde S, Grethe J, Taylor D, Potkin S, FIRST BIRN (2005 submitted) A General XML Schema and Associated SPM Toolbox for Storage and Retrieval of Neuro-Imaging Results and Anatomical Labels.

Human Imaging Database (HID) Human Imaging Database (HID) System 1.6.3

dyounes@stage.nitrcce.org (Danny Younes) — Fri, 27 Jun 2008 22:20:00 GMT

The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large.

The HID system is comprised of the HID Schema (in Oracle and PostgreSQL), the HID Graphical User Interface enabling the navigation through the HID and experimental hierarchies, and lastly the Clinical Assessment Layout Manager (CALM) coupled with General Assessment Manager Engine to manage and integrate clinical data. All components of the HID system can be found by clicking the Download link.

The complete system is used to manage and query local data at various research sites within BIRN. In addition to local operations, the system allows for mediated queries across multiple federated databases allowing researchers to discover data across all relevant sites. The current system provides an intuitive and easy to use clinical and/or derived data complex query builder, query result export for statistical analysis tools, statistical analysis of query results through the BIRN Portal, MRI image preview, conversion and download of the imaging data, as well as integration with BIRN Portal tools for data management and manipulation. Additionally, the system is being developed to provide a complete data management solution where all information regarding a subject can be maintained. A majority of the source code is generated from the database schema itself, allowing changes of the database schema to be reflected in the system easily. Development of the system continues to be a coordinated and parallel effort across multiple BIRN sites. The deployed architecture provides the extensibility, maintainability, security and parallel development features as demanded by the participating BIRN sites for building, accessing and maintaining their human brain imaging and related clinical data.

This latest release contains a new build installation file with updated PostgreSQL Data-Backup scripts.

Human Imaging Database (HID) Upload GUI 1.0

dyounes@stage.nitrcce.org (Danny Younes) — Wed, 22 Oct 2008 21:08:00 GMT

This graphical interface can be used to automatically create upload-template-XML files that can be fed into the data upload scripts.

Please visit the www.nbirn.net page for the latest information.

Human Imaging Database (HID) Data Upload Scripts 1.0

dyounes@stage.nitrcce.org (Danny Younes) — Wed, 09 Jul 2008 17:09:00 GMT

The Upload scripts work in concert with the SRB, XCEDE, and the standardized data hierarchies to put data onto the SRB and link it to the appropriate database.

Organizing and locating information, both clinical metadata and imaging information, in a distributed data environment can be challenging. Because each site in the collaboratory maintains its own linked data storage, it's very important to develop standards for how and where the images are stored, metadata descriptions of what the images are, and how to find them.

To address these requirements the BIRN has implemented standardized data storage hierarchies on the distributed data grid (SRB). The data storage hierarchy was designed to be amenable to automated processing scripts and robust enough to account for differences in storage requirements across BIRN consortia. Not only the physical organization of files is maintained but XML based descriptors of what the files mean to aid in data analysis.

The process of getting imaging information into the standardized data storage hierarchies, the creation of XML based metadata about the data acquisition, conversion of scanner specific, proprietary, data formats into standard "useable" formats, and the linkage of the data locations within the distributed file system into a site's human imaging database (HID) are the goals of the data upload scripts.

Once the data has been "uploaded" using these scripts any site in the collaboratory can locate the datasets by querying their local site's HID database for particular imaging parameters, protocol specifications, or clinical metadata and download the images for further analyses. Using this decentralized approach, the BIRN has put the sites in control of their data while still maintaining shareability and access to the information.