Brain Imaging

Recording Brain Activity

With imaging techniques, such as electroencephalography (EEG), magnetoenzophalography (MEG) or functional magnetic resonance imaging (fMRI) the processes in the brain can be investigated. Brain activity can be recorded even directly or indirectly and interpreted by a computer system.

Ultra High-Field MRI system: 9.4 T MR whole body system

For the investigation of the reaction of the brain to different kinds of stimulation, the scanner is equipped with a visual, auditory and tactile stimulation system. The optical stimulation setup for functional MRI and functional MRS available at the 9.4 T human MRI scanner consists of a projector and a mirror system combined with stimulation software.

Due to the increased signal-to-noise ratio it is possible to acquire functional and anatomical images of the human brain with sub-millimeter spatial resolution. For this reason, the limiting factor of the resolution often is the motion of the subject. Even with careful padding, smallest displacements due to breathing or heartbeat cannot be avoided. To overcome this problem, we are using a motion tracking system from Kineticor. It consists of a camera mounted in the scanner bore and a moiré phase marker attached to the subject’s head. The system has a tracking precision of up to 10 µm / 0.01° at a frame-rate of 80 Hz. The recorded subject motion is used to adapt the image slice position and orientation in real time during the experiment.

Ultra High-Field MRI system: 14.2 T small animal system

This scanner was delivered in August 2007 with a field strength of 16.4 T, at that time the strongest field in a horizontal MRI instrument worldwide. The magnet was built by Magnex (Oxford), the MR hardware was delivered by Bruker Biospin in Ettlingen. After four years of successful operation, it was damaged by a quench in October 2011, and had to be sent to Oxford for repair. Since August 2013 the scanner is back in service, now with a reduced field strength of 14.1 T. It is equipped with gradients that are able to reach a strength of 1 T/m within 181 µs and a high-performance shim system with nine first and second order shim channels. Its inner diameter of 12 cm makes it possible to insert extensive equipment for brain stimulation or multi-modality experiments or to examine even larger animals like small monkeys.

Recently, the spectrometer hardware was upgraded to the current Bruker Neo system and is now running ParaVision 360, allowing to perform dual-channel pTx and dynamic shimming. A wide variety of homebuilt MR-coils includes surface coils for rat brain imaging, large quadrature transmit/receive birdcage coils for investigating samples or entire rats, or double-tuned transmit and receive coils for deuterium imaging.

Clinical MRI: 3 Tesla MRI whole body system

The clinical 3 T scanner is based on a Siemens Trio magnet, upgraded to a state-of-the art Siemens Prisma system. It has a bore diameter of 60 cm and is capable of signal reception on 64 channels simultaneously for parallel imaging. The gradients have a maximum strength of 80 mT/m with a slew rate of 200 T/m/s and are equipped with a 2nd order shim system. Due to the high gradient fidelity, it is also well suited for diffusion weighted MRI. In addition to projects from our department, this scanner is used extensively for functional imaging studies performed by other groups from our institute as well as external collaborators from the University of Tübingen.

The 3T laboratory is equipped with state-of-the-art stimulation systems for investigation of visual, auditory and tactile senses by use of functional magnetic resonance imaging techniques. Additionally, the scanner can be combined with an MR compatible EEG System (Contact Precision Instruments, London, UK) allowing simultaneous acquisition of EEG and functional magnetic resonance data.

Low Field MRI 

Another area of interest at the Magnet Resonance Center, here at the institute, is ultralow-field magnetic resonance imaging (ULF MRI). For studies on phantoms and small animals, a ULF MRI laboratory is installed since 2015. In contrast to conventional or high-field MRI no helium cooled magnet is needed. Instead a helium cooled SQUID (Superconducting QUantum Interference Device) based broadband detector is used, which is extremely sensitive. Therefore, the ULF MRI system sits inside a three layered shielding chamber, which is capable of shielding low and high frequency noise sources.

The ULF MRI system was designed within the Department for High field Magnetic resonance from the research group for Ultralow Field Magnetic Resonance Imaging. It was fabricated by the internal mechanics workshop. The system is also equipped with home-made amplifiers, fabricated by the electronics workshop.

Until now, novel hyperpolarization techniques are investigated, which may enable high resolution imaging at ULF. The necessary sequences are programed via Labview and the signals are fed into the amplifier with a National Instruments PXIe system.

Coil Laboratory

Experiments with the ultra-high-field scanners are enabled by homebuilt rf-coils, preamplifiers and T/R-switches. This hardware is designed and constructed in our coil laboratory, equipped with two network analysers, a noise figure analyser, a spectrum analyser and a shielded box for noise figure measurements.

In addition, several software Packages for simulation of coils (XFDTD, Remcom; SEMCAD, Speag; Microwave Studio, CST) and preamplifiers (Microwave Office, Applied Wave Research, El Segundo, CA, USA) are available.

LED/Laser laboratory in combination with fMRI

The laser lab is built up in combination with high field fMRI of 14.1T scanner. Two separate rooms are included for laser laboratory. The first one is set for animal preparation and electrophysiology/ calcium recording. The second room is build close to the 14T scanner so that we can establish the optical imaging/ recording environment inside the 14T magnet bore. To build up the optical/fMRI multi-modal platform, we first designed open double-ring transmitter coil to allow the sufficient space inside the 12cm gradient and supplement with surface coils (2mm to 2cm diameter) built-in-house for rodents. Figure 1 shows the first generation of the light path to record the GCaMP6-mediated calcium signal through fiber optic. Figure 2 shows the second generation two-channel light path system to simultaneously record the fluorescent calcium signal and fMRI signal from the animal brain.

The physiological monitoring system for small animal fMRI has been implemented in combination with the optogenetics. The viral vectors are acquired primarily from the Upenn vector core with specialized custom design. We have three Laser systems at 470nm, 590nm, and 360nm from CNIlaser. For simultaneous fiber optic-mediated calcium recording with fMRI, we have built up our own optic system for recording.

For simultaneous acquisition of widefield optical imaging and MRI, an in-bore optical imaging system was developed, based on a custom-built, magnetic field proof scientific CMOS camera by PCO (Weilheim, Germany). Together with high-performance optical components, modified to be used during MRI experiments, and an in-built surface coil makes it possible to acquire intrinsic optical imaging data while running fMRI (Figure 3). Further applications, like imaging of brain activity using Ca2+ or voltage sensors are possible.

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