Name: standardized data acquisition for neuromelanin-sensitive magnetic resonance imaging of the substantia nigra
Uploaded: 2021-09-08T13:00:00
Description: Watch this Scientific Journal Video about Standardized Data Acquisition for Neuromelanin-Sensitive Magnetic Resonance Imaging of the Substantia Nigra at JoVE.com

Dr. Horga received support from the NIMH (R01-MH114965, R01-MH117323). Dr. Wengler received support from NIMH (F32-MH125540).

NOTE: The research conducted to develop this protocol was performed in compliance with New York State Psychiatric Institute Institutional Review Board guidelines (IRB #7655). One subject was scanned for recording the protocol video, and written informed consent was obtained. Refer to the Table of Materials for details about the MRI scanner used in this protocol.
1. MRI acquisition parameters
<ol>
	<li>Prepare to acquire high-resolution T1w images using a 3D magnetization pre...

The dopaminergic system plays a crucial role in healthy cognition and neuropsychiatric disorders. The development of noninvasive methods that can be used to repeatedly investigate the dopaminergic system in vivo is critical for the development of clinically meaningful biomarkers. The protocol described here supplies step-by-step instructions for acquiring good-quality NM-MRI images of the SN, including placement of the NM-MRI volume and quality control checks to ensure usable data.
Ev...

Neuromelanin (NM) is a dark pigment found in dopaminergic neurons of the substantia nigra (SN) and noradrenergic neurons of the locus coeruleus (LC)1,2. NM is synthesized by the iron-dependent oxidation of cytosolic dopamine and norepinephrine and is stored in autophagic vacuoles in the soma3. It first appears in humans around 2-3 years of age and accumulates with age1,4,5.
Within the NM-containing vacuoles of SN and LC neurons, NM forms complexes with iron. These NM-iron complexes are paramagnetic, allowing for noninvasive visualization of NM using magnetic resonance imaging (MRI)6,7. MRI scans that can visualize NM are known as NM-sensitive MRI (NM-MRI) and use either direct or indirect magnetization transfer effects to provide contrast between regions with high NM concentration (e.g., the SN) and the surrounding white matter8,9.
Magnetization transfer contrast is the result of the interaction between macromolecular-bound water protons (which are saturated by the magnetization transfer pulses) and the surrounding free water protons. In NM-MRI, it is believed that the paramagnetic nature of NM-iron complexes shortens the T1 of the surrounding free water protons, resulting in reduced magnetization-transfer effects so that regions with higher NM concentration appear hyperintense on NM-MRI scans10. Conversely, the white matter surrounding the SN has a high macromolecular content, resulting in large magnetization-transfer effects so that these regions appear hypointense on NM-MRI scans, thus providing high contrast between the SN and surrounding white matter.
In the SN, NM-MRI can provide a marker of dopaminergic cell loss11 and dopamine system function12. These two processes are relevant for several neuropsychiatric disorders and are supported by a vast body of clinical and preclinical work. For example, abnormalities in dopamine function have been widely observed in schizophrenia; in vivo studies using positron emission tomography (PET) have shown increased striatal dopamine release13,14,15,16 and increased dopamine synthesis capacity17,18,19,20,21,22. Furthermore, post-mortem studies have shown that patients with schizophrenia have increased levels of tyrosine hydroxylase&#8212;the rate-limiting enzyme involved in dopamine synthesis&#8212;in the basal ganglia23 and SN24,25.
Several studies have investigated patterns of dopaminergic cell loss, particularly in Parkinson&#39;s disease. Post-mortem studies have revealed that the pigmented dopaminergic neurons of the SN are the primary site of neurodegeneration in Parkinson&#39;s disease26,27, and that, while SN cell loss in Parkinson&#39;s disease is not correlated with cell loss in normal aging28, it is correlated with the duration of the disease29. Unlike most methods for investigating the dopaminergic system, the non-invasiveness, cost-effectiveness, and lack of ionizing radiation make NM-MRI a versatile biomarker30.
The NM-MRI protocol described in this paper was developed to increase both within-subject and across-subject reproducibility of NM-MRI. This protocol ensures full coverage of the SN despite the limited coverage of NM-MRI scans in the inferior-superior direction. The protocol makes use of sagittal, coronal, and axial three-dimensional (3D) T1-weighted (T1w) images, and the steps should be followed to achieve proper slice stack placement. The protocol outlined in this paper has been utilized in multiple studies31,32 and was extensively tested. Wengler et al. completed a study of the reliability of this protocol in which NM-MRI images were acquired twice in each participant across multiple days32. Intra-class correlation coefficients demonstrated excellent test-retest reliability of this method for region of interest (ROI)-based and voxelwise analyses, as well as high contrast in the images.

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	<tbody>
		<tr>
			<td>3T Magnetic Resonance Imaging</td>
			<td>General Electric</td>
			<td></td>
			<td>GE SIGNA Premier with 48-channel head coil</td>
		</tr>
	</tbody>
</table>

standardized data acquisition for neuromelanin-sensitive magnetic resonance imaging of the substantia nigra

The dopaminergic system plays a crucial role in healthy cognition (e.g., reward learning and uncertainty) and neuropsychiatric disorders (e.g., Parkinson's disease and schizophrenia). Neuromelanin is a byproduct of dopamine synthesis that accumulates in dopaminergic neurons of the substantia nigra. Neuromelanin-sensitive magnetic resonance imaging (NM-MRI) is a noninvasive method for measuring neuromelanin in those dopaminergic neurons, providing a direct measure of dopaminergic cell loss in the substantia nigra and a proxy measure of dopamine function. Although NM-MRI has been shown to be useful for studying various neuropsychiatric disorders, it is challenged by a limited field-of-view in the inferior-superior direction resulting in the potential loss of data from the accidental exclusion of part of the substantia nigra. In addition, the field is lacking a standardized protocol for the acquisition of NM-MRI data, a critical step in facilitating large-scale multisite studies and translation into the clinic. This protocol describes a step-by-step NM-MRI volume placement procedure and online quality control checks to ensure the acquisition of good-quality data covering the entire substantia nigra.

Figure 4 shows the representative results from a 28-year-old female participant with no psychiatric or neurological disorders. The NM-MRI protocol ensures complete coverage of the SN, achieved by following step 2 of the protocol&#160;outlined in Figure 1, and satisfactory NM-MRI images by following step 3 of the protocol. Excellent contrast between the SN and neighboring white matter regions with negligible NM concentration (i.e., crus cerebri) can be seen. Thes...

Watch this Scientific Journal Video about Standardized Data Acquisition for Neuromelanin-Sensitive Magnetic Resonance Imaging of the Substantia Nigra at JoVE.com

Standardized Data Acquisition for Neuromelanin-Sensitive Magnetic Resonance Imaging of the Substantia Nigra

This protocol shows how to acquire neuromelanin-sensitive magnetic resonance imaging data of the substantia nigra.

The dopaminergic system plays a crucial role in healthy cognition (e.g., reward learning and uncertainty) and neuropsychiatric disorders (e.g., ...

The protocol presents the first standardized and highly-detailed step-by-step procedure for acquiring neuromelanin-sensitive MRI. This will allow the field to directly compare data across sites and combine samples to validate generalized biomarkers. The technique uses a detailed placement procedure and quality control checks to minimize data loss.The technique will facilitate large-scale studies necessary to develop and validate biomarkers in neuropsychiatric disorders, particularly for the diagnosis of Parkinson's disease. It is useful to review the basic concepts in neuroanatomy, such as terms for different planes and locations of the brain that allow one to get oriented, while examining brain images on the scanner console. Start by acquiring a high resolution T1-weighted or T1W image of a maximum one millimeter isotropic voxel size that is aligned along the anterior commissure, posterior commissure or AC-PC line and the midline.Immediately after the acquisition, perform the alignment of the high resolution T1W image through online reformatting with the compatible software. Load the sagittal, coronal, and axial views of the AC-PC-aligned T1W image and ensure that the reference lines depicting the location of each displayed slice are present. Next, visually inspect the sagittal slices of the reformatted image to identify the sagittal image showing the largest separation between the mid-brain and thalamus.Use the sagittal image to visually identify the coronal plane, delineating the most anterior aspect of the mid-brain. In the coronal image, visually identify the axial plane that outlines the inferior aspect of the third ventricle. On the sagittal image, align the superior boundary of the NM-MRI volume to the axial plane identified earlier.Then, move the superior boundary of the NM-MRI volume three millimeters in the superior direction. Similarly, align the NM-MRI volume to the midline in the axial and coronal images and acquire the NM-MRI images. Perform quality control checks on the acquired NM-MRI images by ensuring that the images cover the entire substantia nigra or SN.Confirm that the SN is visible in the central images, but not in the most superior or most inferior images of the NM-MRI volume.If the NM-MRI images fail the preliminary quality control check, repeat the T1-weighted acquisition, NM-MRI placement procedure, and acquisition. Next, visually inspect each slice of the acquired NM-MRI scan to check for artifacts. Check for artifacts that go through the SN and the surrounding white matter.Look for abrupt changes in signal intensity with a linear pattern that does not respect normal anatomical boundaries. NM-MRI images with artifacts resulting from blood vessels should be retained, as these artifacts will most likely always be present. If the artifacts are due to the participants'head motion or are ambiguous, copy the NM-MRI volume placement and reacquire the NM-MRI images.Upon reacquisition, if the artifacts remain present, proceed with these images, as they could be biological rather than a result of motion. The protocol ensures the acquisition of satisfactory NM-MRI images with complete coverage of the SN in a stepwise manner. In the initial quality check of acquired images, the SN was visible in the most superior slice, indicating that full coverage of the SN was not achieved.The images failed the second quality check due to the presence of artifacts resulting from blood vessels, artifacts resulting from motion, or ambiguous artifacts. In the representative analysis, the satisfactory NM-MRI images from most inferior to most superior are displayed. On the images, excellent contrast between the SN and neighboring white matter regions with no neuromelanin concentration could be seen.The procedure ensures that good quality neuromelanin-sensitive MRI data is acquired in a reliable and repeatable fashion. The data can be used to non-invasively investigate dopamine cell loss in neurodegenerative diseases.

Research

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