The overall goal of this procedure is to measure high resolution FMRI signals in the human midbrain and brainstem. This is accomplished by first presenting the appropriate visual stimulus to the research subject. Then an optimal set of FMRI.
Procedures and parameters are used to collect data and the data is analyzed using a combination of standard and surface based analysis techniques. The final step is to overlay the data on A 3D surface representation for visualization. Ultimately, high resolution FMRI is used to show a topographic representation of polar angle to visual stimulation in human superior colus.
The main advantage of this technique over existing methods for subcortical structures is that we are able to achieve a high resolution while overcoming the low signal to noise ratio associated with high resolution FMRI. We are able to do this by using specialized image analysis and acquisition techniques. Although this method was designed specifically to image function in human superior colus, it can also be applied to other subcortical regions such as the lateral ululate nucleus, inferior colus, or subthalamic nucleus.
To obtain a polar angle, retina atopic map in the superior Colus first set up a functional paradigm using a 90 degree wedge of moving dots as the stimulus. The stimulus is divided into two by three virtual sectors with dots in one of the sectors randomly chosen on each trial to move slower or faster than all other dots. Here is a sample trial with the center left sector dots moving faster than dots in other sectors.
After each trial, the wedge rotates around the fixation in 30 degree increments so that the stimulus completes a full cycle with a 24 second period. Each run consists of nine and a half rotations of the stimulus and experimental sessions should include 16 to 18 runs prior to scanning. Have each subject practice the visual task for each two second trial.
Instruct the subject to covertly, attend to the wedge and perform a speed discrimination task While maintaining fixation. Using a button press, the subject should indicate if dots in one of the sectors are moving faster or slower than other sectors prior to scanning standard MRI Safety procedures should be followed. Position the subject on the scanner table and place the RF coil over the head.
Then be sure to secure the subject's head with foam pads to minimize head motion. Explain that FMRI is particularly sensitive to motion artifacts, especially at the high spatial resolutions used in this study. Also place an MRI COMPATIBLE button pad in one hand and give instructions regarding which button to press during the task.
The stimulus is projected onto a display screen viewed using a mirror mounted on the coil. The human superior colus is a small but distinct structure about nine millimeters in diameter located on the dorsal surface of the midbrain and multiple localizer imaging series are required for its precise localization. Run the localizers along sagittal axial and coronal planes.
Now use these localizer images to precisely prescribe the superior colus with eight to 10 contiguous slices. Then obtain high resolution T one weighted structural images using a three-dimensional SPGR sequence. These images will be used to align the FMRI data to a high resolution structural reference volume that should be obtained in a separate session.
Next set up for functional imaging using a three shot spiral trajectory acquisition to obtain an in plain pixel size of 1.2 millimeters. Set the echo time to 40 milliseconds, which is longer than typically used in cortex, corresponding to a longer measured value of T two star set. TR to one second so that a volume is acquired every three seconds.
When ready, begin the scan while running the functional paradigm. Once functional imaging is complete, obtain another high resolution T one structural image series in a separate session. For each subject, obtain a high resolution reference volume using a T one weighted sequence that will provide good tissue contrast.
This sequence will be about 28 minutes long. Once imaging is completed, use a combination of automatic and manual techniques provided in the ITK SNAP software to segment portions of the brainstem and thalamus in the high resolution volume. The cerebrospinal fluid tissue interface of the superior colliculus is interpolated from the segmentation using ISO density tessellation and then refined to produce a smooth, accurate surface representation.
This surface provides vertices and normals that are used for laminar calculations as well as a means to visualize functional data. The analysis described utilizes the Mr.Vista software package as well as tools developed on the Mr.Vista framework. Begin by initializing a session and choosing the option to spatially normalize the intensity of the average data to reduce the effects of coil in homogeneity and discard the first half cycle of images.
To avoid transient MR equilibrium and hemodynamic effects. Then open the Mr.Vista software. Next, perform subject motion and slice timing corrections.
Then average the multiple runs recorded within each session. To improve SNR, align the structural data for the FMRI session to the reference volume. Load the alignment and segmentation into Mr.Vista.
Then transform the functional time series data to the segmented reference volume. The following steps, use tools developed on the Mr.Vista framework. Compute a distance map by calculating the distance between each SC tissue voxel and its nearest vertex on the SE surface.
These distances are used to measure laminar position within the reference volume. Next, perform a laminar segmentation process to enable depth averaging of time series data to improve the SNR. For each point on the SC surface, use these laminar associations to average the time series over a specified depth range to analyze the topographic representation of the data.
Perform coherence analysis on the depth average time series by fitting a sinusoid at the stimulus repetition frequency for each voxel from this fit derive surface maps of response, amplitude, coherence, and phase. The phase of the sinusoidal fit will measure the position of the stimulus. Here we see phase data overlaid on a 3D surface of the SC zero phase corresponds to the upper vertical meridian.
The stimulus then rotates clockwise, so a pie over two phase corresponds to when the stimulus has rotated to the horizontal meridian in the right visual field. After PI radian of phase, the stimulus crosses into the left visual field and so forth. The response to visual stimulation is represented Contral laly in the SC IE, the left visual field is represented on the right SC and vice versa.
Boundaries of the entire superficial extent of the SC are marked by red dashed lines. There is a topographic organization of the activity. The right upper visual field is represented medially on the left colus and the lower field is represented laterally.
Similarly, the left upper visual field is represented medially on the right, colliculus and lower is represented laterally. After watching this video, you should have a good understanding of how to perform high resolution FMRI in human midbrain and brainstem in particular, you should be able to understand how to present a visual stimulus. Collect high resolution FMRI data, perform standard and surface based analysis, and finally render the data on a 3D surface to obtain Tino topic maps on the surface of superior colliculus.
