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

In operation since July 2007, this scanner is the third MR system worldwide with this field strength, the first in Europe and the first 9.4 T scanner built by Siemens. The magnet itself weighs 48 tons and the bore diameter is 82 cm without the gradient coil required for spatial encoding. It has a usable bore size of 60 cm and a head gradient with a maximum gradient strength of 60 mT/m and a slew rate of 400 T/m/s. Its length is almost 4 m and it is placed inside a cage consisting of 600 tons of steel for shielding the magnetic field. This scanner is equipped with a broadband amplifier for multi-nuclei excitation. Hardware for excitation and acquisition, like rf-coils and preamplifiers, are designed and built in our institute.

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

This scanner was delivered in August 2007. With a field strength of 14.2 T and a free bore size of 12 cm, it has the strongest horizontal MR magnet worldwide. The 25 tons magnet with 26 cm bore is accommodated in a 220 tons tempered steel enclosure to shield the stray field. It was built by Magnex Scientific (Oxford, UK), the MR hardware was delivered by Bruker Biospin in Karlsruhe. The system is equipped with gradients with a strength of 1 T/m and a high-performance shim system with dynamic shim capacities. State-of-the-art animal handling and supervision equipment is used to prepare the animals for the experiments, to ensure their well-being during anaesthesia and to monitor their physiological parameters during the measurements.

Clinical MRI: 3 Tesla MRI whole body system

Siemens 3T whole body system

In 2013 the Siemens Tim Trio research system was upgraded to a Siemens PRISMA system with a magnetic field strength of 3 T and a bore diameter of 60 cm. It is capable of signal reception on 64 channels simultaneously for parallel imaging and is equipped with 80 mT/m gradients with a slew rate of 200 T/m/s and a 2nd order shim system. This scanner is mainly used for functional imaging studies performed by groups of our institute as well as external collaborators from the University of Tübingen, but is also well suited for diffusion weighted MRI due to the high gradient fidelity. The 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 a MR compatible EEG System (contact precision instruments, London, UK) allowing the simultaneous acquisition of EEG and functional magnetic resonance data.

Low Field MRI 

Lab for Ultralow Field Magnetic Resonance Imaging

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

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

Figure 1. The calcium recording setup.
Figure 2. The schematic drawing of the two-channel calcium recording setup with simultaneous fMRI. B. The time courses of simultaneous SSFP fMRI signal from bilateral FP-S1 and neuronal (left) and astrocytic (right) Ca2+ signal with bilateral FP electric stimulation (3 Hz, 4 s, a representative figure at 2.0 mA). The middle panel is color-coded BOLD-fMRI map with bilateral FP-S1 activation.

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.

Figure 3. Setup for simultaneous widefield optical imaging and MRI. Top: Drawing of setup inside the scanner bore. Bottom: Photograph of actual setup.

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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