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MIDAS eNewsletter

 

February, 2007

New MIDAS

 

·        Linux: A ‘release’ for Linux is available. Note, MIDAS is not tested under OS emulators, e.g. VMWare under Linux or Unix, and this is not recommended.

·        Agreements: Our software distribution agreement and data sharing agreement have been developed. I will be asking all sites to complete the software agreement (I will try to get our Technology Transfer office to come up with a simpler license agreement).

·        REFDAT now includes estimation of a T2* map from the water signal. This will be evaluated as a method to generate the mask used for the spectral fitting, to avoid spending time fitting voxels in inhomogeneous regions. Thanks to Dan Spielman for that idea. Additional options have been added so any existing processing files for this application should be checked and resaved.

·        FDFT has undergone some (largely cosmetic) changes on the phase-array reconstruction, but this means that processing parameters (for phase-array data) should be checked and the proc-files re-saved before using.

·        Multi-TE MRSI: The MRSI processing now supports multi-TE SI, e.g. for spatially-resolved and 2D J-resolved MRS.

·        SINorm: The SI signal normalization now includes a separate normalization factor for the water-reference image, in addition to that used for the metabolite signal normalization. This is not meant to provide a quantitative measure, but has been added just to get the numbers into a reasonable range.

·        Registration: A new version of the non-linear spatial registration is currently under evaluation and should be in the next major release.

·        Viewer: A new version of the MIDAS Viewer is available that makes use of ImageJ, providing access to many existing image processing functions. This work is being done by James Norman “JC”, who is now working with Jeff Alger, and we welcome him to the effort.

·        Segmentation: Now includes an option for correction of the bias field in the input MRIs.

·        SVS: Support for single voxel spectroscopy and spectral fitting is now initiated though a separate icon on the toolbar: Description: icon_svs.  The “Vespa” spectral fitting program is provided courtesy of Brian Soher and documentation has been provided by Dr. Govindaraju and Rajesh Garugu.

MIDAS Tips

 

Updates: The MIDAS software is changing continuously and I recommend updating regularly. This can be obtained from the following web links:

http://midas.med.miami.edu/Downloads/Midas_Release_Windows.zip    [ Windows STABLE version ]

http://midas.med.miami.edu/Downloads/Midas_Latest_Windows.zip        [ Windows TEST version ]

http://midas.med.miami.edu/Downloads/Midas_Release_Linux.zip         [ Linux STABLE version ]

http://midas.med.miami.edu/Downloads/Midas_Latest_Linux.zip           [ Linux  TEST version ]

All versions require the usual password. Typically, "stable" versions are updated when a major change is implemented, whereas the "test" version is updated at least weekly and incorporates all ongoing fixes.

Since this pre-release version of the software is still undergoing significant changes, it is recommended that you update the installation frequently. I update weekly, and to simplify this I created a desktop icon (Windows) with the Target pointing to the web link. E.g. “Explorer http://midas.med.miami.edu/Downloads/Midas_Latest_Windows.zip”

It’s fully automated, just a few clicks and everything is updated. The only additional recommended step is to set the shortcut to start IDL in Minimized mode. In Windows, this is done by Right Click on the icon -> Properties -> Run -> Minimized.

Documentation: All Help files and other documents are provided with the distribution, but now it can also be found on-line at: http://midas.med.miami.edu/Documents  

Java Error Messages under IDL: The MIDAS programs make extensive use of calls to Java programs through the “JavaBridge”. One limitation of this method is that error messages generated in the Java code are only visible in the IDL Output Log window once the DOS shell (under Windows) has been closed. Furthermore, if you run IDL minimized (which is recommended), then you will have to restore the IDL window to read the messages.

If you have questions that you would like to see discussed then please send them in.

EPSI WIP

 

 

We have a preliminary version of our volumetric EPSI sequence running under VB13. Thanks to Sulaiman Sheriff (Miami) and Brian Dale of Siemens for this monumental effort. There were some major changes required. If you are using this sequence on the TIM and planning to move to VB13, one requirement is to have at least 16Gb RAM on the MRIR computer, and 20Gb are recommended. Some TIM systems in the US have only 8Gb RAM.

The Importer has also been modified to support the new Dicom format.

Developer’s Corner

 

Data_FormatParameter:  This parameter has been added to the XML descriptors to describe an image format. In principle the MIDAS data management system can handle any file format that is in the form of a header+binary data, although the MIDAS software updates parameters only in the XML. Processed data must be specifically “Exported” to accurately support some other format. Currently, MIDAS only supports DICOM on import and Analyze for export. It is primarily the Statistics program (MSTAT) that makes use of Analyze format data. There remains some ambiguity on the support for Analyze since the image orientation generally differs from that of DICOM, which MIDAS uses and a clearer definition of the support for this file format will be developed.

Subject.XML file lock: To support distributed processing, where multiple processes may wish to access the same subject parameter information simultaneously, a “lock” function has been implemented on the Subject.xml file. Since we have not found a standard method in Java for opening a file with exclusive access, the following method has been implemented. The first time an application initiates a write or modify to the subjectXML, a file named subject.lock is automatically created. If this file is present during another attempt to write or modify the subject, then that open is delayed until the .lock file is deleted, which occurs when the object is released. If the .lock file remains then the OpenFile command will timeout in 30 seconds and an error will be returned.  It is important to note that multiple applications can open the subjectXML for read access, but that only one can have it open for modification.

A problem can occur if the program crashes before deleting the subject.lock file, which effectively blocks any application from opening the subject.xml file. If your program returns an error saying that it cannot open the subject.xml file, or hangs without any error, then check for this situation and delete the subject.lock file if it is there.

XMLCompare: This is a Windows application developed specifically to assist in debugging the subject.xml.  The tool allows comparison of two or more xml files on a node by node basis. This is useful for checking which parameters have been changed, e.g. by comparison against a copy of an earlier version of the subject.xml file, or looking for differences between two datasets. The example shown below illustrates differences in parameters under the SI Series node for two subjects:

This application will be included in the next release as a self-extracting zip file, but as this is meant as a developer tool it will not be incorporated into the MIDAS toolbar and must be installed and run directly.

Web Site: The MIDAS Web site has been modified to work with Non-Explorer Browsers, although the Login still requires MS Internet Explorer.

Now included on the site is a list of metabolite chemical shifts and J-coupling values, taken from the NMR in Biomedicine paper from Dr. Govindaraju. We have obtained permission from the publisher to make this available on the web and future plans include updating this with measurements from other papers or research groups.

We would like to expand the content of this web site and contributions would be welcome.

Other, Ongoing, and Plans

 

·        Parallel MRSI reconstruction using SENSE and other algorithms is currently being implemented.

·        The Competing Continuation of the NIH grant has been submitted.

More Midas

 

Description: MIDAS Asteroid
Trajectory for Asteroid “1981 Midas”

Original link: http://neo.jpl.nasa.gov/cgi-bin/db_shm?sstr=midas

 

 

Andrew Maudsley

February 2007

 

This newsletter is aimed at providing information to the developers and users of the MIDAS software package. If you would prefer not to receive notification of these reports just let me know (amaudsley@med.miami.edu).