Lecture 3: Neuroimaging

Measuring the brain

Measuring the brain and its activity can be done in different ways. To create anatomical imagines and by that measuring the brain structure X-rays, MRI, D-MRI and MRS are commonly used techniques. CT and angiography are X-rays techniques. MRI is used to differentiate different tissue types. D-MRI is used to measure diffusion through white matter tracts and MRS is used to measure chemical compositions.

The brain’s activation and with that the brain’s function can be measured both directly and indirectly. Direct techniques (neuronal firing) are EEG, MEG, ECoG and invasive line electrodes. Indirect techniques (blood circulation or oxygen levels) are fMRI, PET (3D) and fNIRS (2D).

Techniques to stimulate the brain and measure perturbing brain functions are DBS, (r)TMS and TDCS.

Brain structure: X-rays

The technique of X-rays was the first way of looking into the body without having to open it up. Bone structure can be see very clearly. Radiographs are the rays that are absorbed to a different extent by different tissue types and different doses of radiation. Soft tissue cannot be seen when using the X-rays technique.

CT is an example of an X-rays technique. It has a moderate dose of radiation and by creating multiple projections the result will have a better resolution. A CT-scan is a radiograph from different angles. Soft tissue cannot be seen when using this X-rays technique.

Angiography is an X-rays technique to image blood vessels by using contrast agents.

Brain structure: MRI

MRI is based on magnetic fields and does not use radiation. Contrast agents are sometimes useful, but not necessary. MRI also imagines soft tissue. Given contrasts by MRI are tissue characteristics, water diffusion and oxygen saturation. MRI consists of a nuclear magnetic resonance: spins of hydrogen atoms/protons are measured. It is used to apply pulses and see what the protons do. Proton density differs over tissue times and they behave somewhat different in tissue types. T1 is a technique used to measure how long it takes for the protons to recover and to go back to their old positions after removing the magnetic field. T2 is a technique used to measure how long the protons twist in direct X and to measure the protons that stop turning in synch to track lesions.

MRI equipment consists of a magnet, a gradient coil (to localize the signal) and a radio frequency coil (to apply pulses to make the protons move, it also receives signals produced by the protons). You can manipulate different aspects to receive different kinds of contrasts. Performing a MRI scan is done by doing the following:

1. Provide a strong, magnetic, constant field. By doing this hydrogen atoms will align through polarization.
2. Excite the protons’ spins using a radiofrequency transmitter, using the right frequency to create precision.
3. Change the magnetic field to identify the location of the outgoing signal.
4. Use a RF coil to measure the signal by adjusting TR (time to repetition, cycle of RF pulses) and TE (time to echo, refocusing spin magnetization)

T1 weighted scans give a good constrast between grey and white matter. It has a short TR and TE. Dark areas on the T1 scan represents cerebrospinal fluid, dense bones and air. Bright areas represent fat.

T2 weighted scans give a good contrast between cerebrospinal fluid and brain tissue. It has e long TR and TE. Bright areas represent cerebrospinal fluid and dark areas represent fat and air. T2 is a technique which is often used in clinical settings, since damage to the brain can cause increased cerebrospinal fluid.

Brain structure: Diffusion weighted MRI (D-MRI)

D-MRI is used to get an idea where certain molecules flow freely and where they are restricted. Diffusion Tensor Imaging (DTI) is a technique used to measure fractional anistorphy (the preferred direction of water in a given voxel) and to measure diffusivity (the average rate of diffusion across the voxel). Diffusion Spectrum Imaging (DSI) also measures these things, but uses more gradients (about 100) than the DTI technique, which uses only 6. The main goal of D-MRI is to look for connection dysfunctions.

Brain function: fMRI

fMRI is a technique used to measure oxygen levels by using a BOLD response (blood oxygen level dependent). This means the scans are longer than other techniques, which gives 4D data. Shorter scans lead to lower spatial resolution or fewer slices. The images produced by fMRI are overlays of a standard structural image and a statistical map indicating where differences are found.

Brain function: blood flow, PET/SPECT

The PET/SPECT technique is used to image blood flow patterns using gamma rays (subtraction method). It is often used in oncology and cardiology. Mixtures of different radioactive isotopes are inserted into the human body by either breathing or shots. Reduction of these substances will be measured over time and changes in pH, glucose, oxygen level, neurotransmitters and proteins will be tracked too. A downside of this technique is that it is very expensive.

Brain function: fNIRS

fNIRS stands for Functoinal Near Infra-Red Spectroscopy and it is used to image blood flow patterns. This technique can identify when and with what specific stimulus a specific brain area will be activated. The images produces by an fMRI are more detailed, but actually doing the scan will take longer, therefore it is not suitable for children, because they have to lay still for a longer period of time. When fNIRS is used, a device will placed onto the scalp and it will measure cortical activity through light absorption of blood.

Brain function: EEG

When using an EEG electrodes will be placed onto the scalp. It measures summated post synaptic potentials (Hertz). Different patterns are associated with different kinds of behaviour. Epilepsy and brain damage can be measured by using an EEG and cognitive brain functions can be tracked too. A downside of this technique is that it hardly gets any data from deep sources and many trials are needed to get reliable stimulus-related signals.

Brain function: MEG

The MEG technique is more precise than the EEG technique. By creating an electric field neuronal activity will create a magnetic field. MEG is better with deep sources and source estimation than EEG. Superconductiong quantum interference device (SQUID) is to detect weak magnetic fields of the brain. Artifacts for this technique are metal, heartbeat, traffic and traffic. It is often co-registered with T1 MRI to estimate sources of activation.

EEG and MEG can be combined to get complementary information. EEG can be combined with fMRI to combine spatial and temporal information.

Brain function: ECoG

ECoG is a technique used to measure directly from the scalp. A grid of electrodes will be placed directly onto the scalp. It is a very common procedure used before epileptic surgery.