Major new release: SequenceTree 4.2.1
From Sequence Tree
April 4, 2009
I am pleased to announce the release and immediate availability of a major new version of SequenceTree and related software. This new release includes the following new capabilities:
- Improved interfacing to the Siemens protocol and user interface, so that both standard and special parameters can be set and retrieved by the sequence.
- Improved interfacing to the Siemens online reconstruction system, enabling online reconstruction for SequenceTree sequences with simple 2D and 3D acquisition schemes.
- New tools for automatic parsing of raw data, for both SequenceTree and non-SequenceTree sequences.
- New tools for automatic real time parsing of raw data (during the scan), enabling efficient and automatic offline reconstruction.
In addition, SequenceTree 4.2.1 is now built on the very latest version of the Qt libraries (i.e. Qt 4.5.0). The installation procedure has changed slightly, so please visit the wiki for detailed instructions.
Contents |
ONLINE RECONSTRUCTION VERSUS OFFLINE RECONSTRUCTION FROM RAW K-SPACE DATA
A great dichotomy – whether to perform online reconstruction, and have the images pop up at the scanner console, or whether to gather the raw k-space data and perform offline reconstruction using MATLAB, ChainLink, C++, or other tools. In this section I will argue that there is no clear universal answer to this important question, but that the right choice depends on the application, and the goals and circumstances surrounding the research being conducted.
On the one hand, it is clear that in many cases it is very desirable, and even essential, to have images appear automatically at the scanner console when the scan has completed. For example this is an essential feature for localizer scans. Furthermore, for archiving purposes it is important for reconstructed images to enter into the image database associated with the patient. One could argue that the ultimate goal for any imaging technique is to eventually have a fully automated and fully integrated image reconstruction in place.
However, from the perspective of the researcher developing novel techniques, the convenience of online reconstruction must be weighed against the difficulty of implementation as well as the limitations inherent to the online reconstruction. For example, during technique development (or the prototyping phase), offline reconstruction based on raw k-space data is often the preferred technique since the changing reconstruction algorithm and data exploration can be most conveniently performed using offline tools such as MATLAB. But even after a novel technique has been developed, tested, and optimized, the image reconstruction algorithm may involve non-trivial and non-conventional steps that are again most easily and most effectively implemented in off-scanner environments. Indeed for some novel techniques, it may even be impossible to implement the appropriate image reconstruction algorithm within the Siemens ICE environment.
In summary, there tend to be two schools of thought regarding implementation of image reconstruction algorithms for novel MRI techniques on a clinical scanner. Some researchers refuse to ever look at the raw data, whereas other researchers will always save the raw k-space data, and perform all reconstruction offline. In general, the appropriate choice depends on the type of research being conducted. This new version of SequenceTree (and related tools) recognizes the need to support both online and offline efforts of image reconstruction, with new tools and capabilities addressing both strategies. See below for details.
CONNECTING ST SEQUENCES TO THE SIEMENS PROTOCOL AND OPERATOR INTERFACE
Beginning with version 4.2.1, SequenceTree has a new and improved method for interfacing to standard and special protocol parameters available on the Siemens operator interface. Recall that in previous versions of SequenceTree, this was accomplished using special syntax in the ‘Notes’ tab of the sequence. This method is now obsolete. Instead the interfacing is now done using C++ code in the Root node of the sequence.
‘Special’ parameters are user-defined parameters that appear on the WIP special card of the operator interface, whereas ‘standard’ parameters are parameters that are part of the standard Siemens protocol (e.g. TE, TR, flip angle). For more information on interfacing to standard and special parameters, see the word document available at the ST download site.
ONLINE RECONSTRUCTION FOR BASIC 2D/3D IMAGING SEQUENCES
SequenceTree sequences can now be reconstructed by the default Siemens image reconstruction program. For now, only basic 2D and 3D Cartesian sampling schemes are supported. For more information, see the word document available at the ST download site.
RTST: AUTOMATIC RAW DATA PARSING INCLUDING REAL TIME OFFLINE ACQUISITION
SequenceTree contains a new component for parsing and processing of raw data. The program, named RTST, can be launched from the SequenceTree toolbar. This utility differs in the following significant ways from the older method that SequenceTree used for parsing raw data:
- RTST can be used to parse the raw data for both SequenceTree and non-SequenceTree pulse sequences.
- RTST uses the Mdh header information to parse the raw data, and therefore does not require the user to specify the pulse sequence or pulse sequence parameters.
- RTST can be used on a neighboring computer at the scanner to collect and parse the raw data in real time as it comes off the scanner.
- RTST provides an integrated environment for parsing, processing, and saving experiments.
For more information, see the word document available at the ST download site.
