Turbo-BrainVoyager. Setup guide

Transcription

1 Turbo-BrainVoyager Setup guide Turbo-BrainVoyager (TBV) is a highly optimized software package for real-time analysis and advanced visualization of functional and structural magnetic resonance imaging data sets. The TBV allows quality assurance of ongoing fmri measurements by assessing head motion and by incrementally computing statistical maps as contrasts of a General Linear Model (GLM). Statistical information can be visualized on original slices (multi-slice view as well as in orthographic 3D mode using anatomical scans of the subject). If anatomical data sets of the subject are prepared with BrainVoyager QX prior to the functional measurement, statistical information can be viewed in Talairach space as well as on surface (mesh) representations. TBV allows to select regions-of-interest (ROIs) from any brain view and plots time courses, estimated beta values and event-related averages dynamically. TBV also allows to use machine learning tools to classify and predict distributed patterns of activity ("brain reading"). Due to its computational and visualization capabilities, TBV supports advanced real-time applications such as neurofeedback, brain computer interfaces (BCIs), adaptive experimental designs and neurosurgical monitoring. This guide contains a description how to set up the TBV with a Siemens MRI system and how to use a stimulation software in combination with the TBV. The set up will mainly be described with the use of a Microsoft Windows based MRI system. MRI systems based on other operating systems can easily be adapted from this guide. All the information in this guide are examples how a common setup could look like. Brain Innovation is not responsible for any damage caused by using this guide. In terms of questions or comments use support AT brainvoyager DOT com mail address.

2 Setup overview: The setup of the TBV consist mainly of two parts: The real-time data export of the MRI images and the access to this exported data from another computer. The real-time data export must be activated on the MRI console computer or can be part of special designed sequences in combination with an export tool on the ICE computer. As one can see on the picture above the MRI images are exported in real-time from the MRI console computer to the TBV computer. On the TBV computer all images will be read and processed from a specified folder. It is essential that the MRI console computer exports the images to a shared folder provided by the TBV computer. Otherwise the realtime export could be decelerated because of multiple network queries that are necessary to read the MRI images. We recommend using the latest version of the operating system to benefit from current versions of the underlying sharing protocols. The schematic network structure, which will be described later on, is true for all scanners and operating systems. To ensure a fast and reliable data transmission and processing please verify that all computers that are not necessary for the fmri experiment are excluded from the network or turned off. The more computers are in the network the more probable it is, that a lengthened transmission time can occur. It is recommend to set the power plan of your operating system (if available) to maximum performance. This ensures that the whole processing of the MRI images can be as fast as possible realized. We recommend a minimum of 2GB of working memory, but to reduce calculation and processing time the usage of latest PC hardware should be favored! (This holds for all supported operating systems!)

3 Since software release VB15A, Siemens supports the real-time export of DICOM mosaic images (one file per functional volume). The recommended way by Siemens to turn this functionality on is to use the IDEA command tool after switching in advanced user mode on the console computer (see documentation by Siemens). Unfortunately there seems to be a problem since the IDEA command tool does not save the specified settings properly to disk. As an alternative solution, the respective "config" file "C:\MedCom\config\Ice\IceConfig.evp" may be changed manually, or better, by using the "XBuilder" program that can be started using the Windows "Run" tool. In XBuilder, change the three export parameters "OnlineTargetPort" (to "-1"), "OnlineTargetHostName" (the name or IP of the computer in network receiving data) and "OnlineTargetPath" (to the name of the folder of the computer in the network, e.g. "\\ \rtfmri"). Note that the configuration file is overwritten each time a new patient is registered, i.e. the settings have to be repeated each time you want to use the real-time export for a new subject. Older systems with older software (A-line, like Allegra) require for example the ICE export tool by Nikolaus Weiskopf (WELLCOME Institute, London) producing real-time in ANALYZE format with POS information. Take a look into the support of your operation system to get to know how to enable and access shared folders from other computers via the network. An example network structure (based on Microsoft Windows operating systems) is shown in the image above. The shared folder is provided by the TBV computer and can be reached via its host name or IP. In this case the TBV computer can be reach at \\ Just append the folder name to access the folder directly. Enter the address ( \\ \rtfmri ) into the address line to access the folder.

4 Be sure that the connection between the two computers is established and the computers can reach each other. To ensure that you can use the computer network administration utility Ping (only on Microsoft Windows based systems) which can be accessed from the command prompt (use windows-key + r-key and type cmd ). In this specific example the connection can be tested by typing ping in the command prompt of the TBV computer. As results the ping times will be shown. If the computer cannot be reached Request timed out. will be displayed. If this happens the IT or MRI technician should be asked for further help. After setting up the connection one can define the settings and parameters in the TBV (verify that both computers can reach the defined folder). Example control settings for Siemens data: In order to prepare a TBV file handling the exported Siemens data, you must change the settings in the Data Format tab of the TBV Settings dialog. The "DataType" box must contain the "SIEMENS_DICOM_MOSAIC" selection. You must also fill in the name of the (expected) first file of the functional data, which is similar to "001_000004_ dcm" (set as default). The first part "001" is constant throughout all measurements of a subject including the anatomical "scout" measurements (it is only changed if the same subject is registered in a future session). The second number is the "series" (or "scan") number. The functional data set is series "4" ("000004") and the value "4" must also be set in the "DicomExpectedSeriesNr" field. The third number is usually "1" ("000001") and that number should be set in the "DicomFirstVolumeNr" field (default). This number will change from volume to volume, e.g. "001_000004_ dcm", "001_000004_ dcm", "001_000004_ dcm" and

5 so on. In order that TBV separates the different numbers correctly from the first file name, the "DicomNameDelimiter" must be set to the underscore ("_") symbol (default). Note that one usually needs to change only the "DicomExpectedSerieseNr" (scan) number for the next expected run ("4" in our case) since the other entries should normally not change and are set to correct values as default. If one would, for example, run a second functional run, one should change "4" into "5" in the "Series" field (and in the "FirstFileName" field, but this is not strictly necessary). For further information take a look at the Turbo-BrainVoyager User's Guide. Neurofeedback setup: TBV supports advanced real-time applications such as neurofeedback and brain computer interfaces (BCIs). The feedback will be conveyed to the subject during the experiment. A conceptional overview is shown in the picture below. In most cases a video projector is used to convey a visual feedback to the subject in the scanner. The feedback can be provided by the neurofeedback dialog of the TBV. The neurofeedback dialog allows to select the data from one or more ROIs as the source of feedback information for a subject during an ongoing measurement. It constitutes a simple Brain Computer Interface (BCI) allowing to use different display formats for neurofeedback. The signal from a ROI can be presented in two major formats to the subject, either in thermometer display (also called bar display, see above) or in time course display type. These types can be selected in the Feedback type field by selecting the Activation level

6 bar or Time course plot option, respectively. (The "Pong" options are for special applications not described here). The "Delayed feedback" option allows to calculate a mean feedback signal that can be used for custom feedback displays, i.e. at the end of modulation blocks. The stand-alone tool FeedbackPresenter can be used to provide the feedback. It reads out the generated feedback files of a specified folder and displays it on the screen. Just take a look at the Turbo-BrainVoyager User's Guide for further information about the neurofeedback application. Also the new stimulus application StimulGL can be used to present the feedback to the subject. StimulGl provides stimulus generation and control for fmri and behavioral experiments. It's optimized for creating flexible behavioral experiments supported by a script engine and a plugin framework. For further information about StimulGL visit