Name: a comprehensive protocol for manual segmentation of the medial temporal lobe structures
Uploaded: 2014-07-02T13:00:00
Description: Watch this Scientific Journal Video about A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures at JoVE.com

This research was supported by funds to FD. MM was supported by an IGERT Fellowship under National Science Foundation Grant No. 0903622. The authors wish to thank the Dolcos Lab members for assistance with data collection and preparation.

1. Amygdala
<ol>
	<li>Anterior Slices of the&#160;AMY
	<ol>
		<li>Identify the first slice of the AMY in which the limen insula initially appears, where the white matter connection between the frontal and temporal lobes is continuous and visible30. In the coronal view, use the angular bundle as the inferolateral border of the AMY.</li>
		<li>Locate the optic chiasm as a landmark for the appearance of the AMY. Use the axial and sagittal views to distinguish the AMY in its early slices from the surrounding unc...

Traditionally, manual segmentation has been considered the gold standard by many researchers. Nevertheless, a precise delineation of the individual structures has been complicated by the highly variable morphology of the MTL structures, and by the usually weak MRI contrasts of these structures against the surrounding neural tissue and non-neural areas. Historically, there have been conflicting descriptions in the literature for some MTL structures. In some cases of segmenting the PRC, for example, the collateral sulcus h...

The medial temporal lobe (MTL), a putative area of the highest level of integration of sensory information1, has been a frequent subject of targeted analyses. For example, the hippocampus and the associated parahippocampal areas have been extensively studied in memory research2-5. Also, the role of the amygdala has been frequently emphasized in research examining emotion processing and emotion-cognition interactions6-11. Recently, various MTL regions have also received attention in the emerging field of personality neuroscience, which links the structure and function of these and other brain regions to individual variation in personality traits12. Assessing the anatomy and function of the MTL structures can be important in facilitating diagnosis of degenerative diseases where specific structural and functional anomalies can occur in different MTL structures. For example, in Alzheimer&#8217;s disease (AD), significant atrophy of the entorhinal cortex and hippocampus can be observed13,14, and atrophy of the hippocampus can predict the transition from mild cognitive impairment to AD15. Automatic segmentation algorithms have recently become popular for segmenting cortical and subcortical structures, but as with any tool, these programs inevitably encounter errors in some cases. In such instances a researcher should be equipped with both the knowledge and guidelines to recognize the anatomical borders of the MTL structures. The tendency in the extant literature has been to target individual MTL subregions16-21, with many protocols tending to focus on hippocampus16-19.
Unlike most of the available published guidelines for MTL tracing, the present protocol provides a comprehensive set of guidelines that allow for clear localization of all MTL subregions. Tracing guidelines for the following MTL structures are described: the amygdala (AMY), the hippocampus (HC), the perirhinal cortex (PRC), the entorhinal cortex (ERC), and the parahippocampal cortex (PHC). The AMY and the HC are traced first, and are then followed by the parahippocampal gyrus (PHG) structures. Note that the generic term HC is used here to refer to the HC formation, which encompasses the HC proper, the subiculum, and the posterior segment of the uncus22-24. Also, note that the PHG can be divided into two segments, the anterior portion and the posterior portion. Within the anterior portion of the PHG, it can be further divided into the lateral and medial anterior PHG, whose cortical areas correspond to the PRC and the ERC, respectively. The PHC, the cortical area of the posterior portion of the PHG, corresponds to the parahippocampal cortex proper. For simplicity reasons, we will be using the terms PRC and ERC to refer to the lateral and medial anterior PHG, and PHC to refer to the posterior PHG. The segmentation for each structure begins with a rough localization of the anterior and posterior borders, along with other relevant landmarks, which is then followed by the actual tracing performed slice-by-slice in the coronal plane, in an anterior-posterior/rostro-caudal direction. In all cases, the sagittal and axial sections are closely monitored to assist the localization of anatomical boundaries and landmarks.
The need for such tracing guidelines is also illustrated in figures displaying possible differences between the output of automatic and manual segmentation protocols. The advantage of a protocol that describes all of the MTL structures in the current visual format is that variations in the anatomy (e.g., the collateral sulcus [CS] depth) that can affect border definitions can be described in context with the surrounding anatomy (e.g., the PRC and ERC medial and lateral borders vary in location depending on the depth of the CS25). This might not be clear or understandable to an inexperienced tracer or an experienced tracer who only traces single or separate structures, and to our knowledge, such a visually comprehensive guideline does not exist.
The present protocol is an explicit presentation of guidelines used for MTL tracing in a previous investigation identifying differential contributions from MTL subregions to the memory enhancing effect of emotion26, adapted to higher resolution brain images allowed by recent developments in structural magnetic resonance (MR) imaging. The tracing is illustrated on scans obtained from a healthy volunteer (female, aged 24), using a 3T MR scanner. Anatomical images were acquired as 3D MPRAGE (TR = 1,800 msec; TE = 2.26 msec; FOV = 256 x 256 mm; voxel size = 1 x 0.5 x 0.5 mm) with an acquisition angle parallel to AC-PC. If image data is acquired with a different acquisition angle, such as oblique orientation, the data should be regridded to a parallel or perpendicular orientation to AC-PC, such that anatomical landmark descriptions translate appropriately. The images were then translated to NIFTI format and input into segmentation software27 for manual tracing. Scan data used in the current protocol was collected as part of a study that was approved by the Institutional Review Board, and the volunteer provided written consent.
By drawing information from various separate tracing protocols for these structures18-22,25,28-31, as well as from anatomical analyses and atlases23,32-37, the present protocol presents a comprehensive set of guidelines that address inconsistencies in the extant literature. Complemented by the accompanying visual materials, this work is expected to promote clearer understanding of the MTL structures, and stir up interest of future research in adopting manual segmentation, either as a primary method of MTL tracing or as a supplementary method to automatic segmentation. By providing an accurate, intuitive, and convenient guide for understanding the MTL anatomy, this protocol will help researchers identify the location of all MTL subregions, relative to their neighboring structures, even when only some MTL structures are specifically targeted for analyses. This will not only increase localization accuracy but will also help tracers make informed decisions in cases of morphological variation, which is highly likely in the MTL. These guidelines can be applied to research involving structural and/or functional MRI investigations of the MTL, including volumetric analyses and brain anomaly detection, as well as localizing procedures for functional, anatomical, and tractographic analyses, in healthy groups. The present protocol could also be used to inform segmentation of MTL structures for patients (e.g., patients with atrophy), if the major anatomical landmarks are relatively preserved. Tracing clinical subjects&#8217; data can take additional time and effort, depending on the severity of atrophy and/or anatomical changes.
It is important to consider the distinction between gyri and cortices when defining ROI. Anatomically, gyrus here refers to both white matter and grey matter, while cortex refers to grey matter only. Depending on the intended use of the ROI, segmentations might include white matter or exclude it.
We recommend the tracing to be performed sequentially, substructure by substructure, one hemisphere at a time. Certain software packages27 allow for tracing borders outlined on one slice to be pasted onto subsequent slices, a feature that speeds up the process. It is always advisable to reference the opposing hemisphere as needed, in order to check for consistency across the two sides (e.g., in detecting anatomical landmarks). Alternatively, parallel tracing of the same structures within the two hemispheres can also be performed. Regardless of whether the tracing is sequential or parallel, once the process is complete, the tracers should double-check the end-result and make adjustments as needed, referencing both hemispheres and multiple plane views. Depending on the experience of the tracer and the resolution of the imaging data, manual segmentation of the MTL for healthy subject data can take from 8-10 hr or more, in the case of a novice tracer, to 3-4 hr, in the case of an experienced one.
<img alt="Figure 1" fo:content-width="4in" src="/files/ftp_upload/50991/50991fig1highres.jpg" width="400" /> 
Figure 1. A 3D overview of the MTL, traced using the present protocol. Structures shown here are the AMY (red), the HC (blue), the PRC (yellow), the ERC (pink), and the PHC (green).

<table border="0" cellpadding="0" cellspacing="0" width="836">
	<tbody>
		<tr height="20">
			<td height="20" style="height:20px;">ITK-SNAP</td>
			<td>ITK-SNAP Team at University of Pennsylvania and University of Utah</td>
			<td>ITK-SNAP v2.2</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">FSL</td>
			<td>Functional Magnetic Resonance Imaging of the Brain (FMRIB) Analysis Group</td>
			<td>FSL v4.1</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">3T Siemens Trio MR Scanner</td>
			<td>Siemens</td>
			<td>3T Trio</td>
			<td></td>
		</tr>
	</tbody>
</table>

a comprehensive protocol for manual segmentation of the medial temporal lobe structures

The present paper describes a comprehensive protocol for manual tracing of the set of brain regions comprising the medial temporal lobe (MTL): amygdala, hippocampus, and the associated parahippocampal regions (perirhinal, entorhinal,&#160;and parahippocampal proper). Unlike most other tracing protocols available, typically focusing on certain MTL areas (e.g., amygdala and/or hippocampus), the integrative perspective adopted by the present tracing guidelines allows for clear localization of all MTL subregions. By integrating information from a variety of sources, including extant tracing protocols separately targeting various MTL structures, histological reports, and brain atlases, and with the complement of illustrative visual materials, the present protocol provides an accurate, intuitive, and convenient guide for understanding the MTL anatomy. The need for such tracing guidelines is also emphasized by illustrating possible differences between automatic and manual segmentation protocols. This knowledge can be applied toward research involving not only structural MRI investigations but also structural-functional colocalization and fMRI signal extraction from anatomically defined ROIs, in healthy and clinical groups alike.

Illustration of Possible Differences between Manual and Automatic Segmentation
A 3D model of the manual segmentation for the AMY, HC, PRC, ERC, and PHC is shown in&#160;Figure 1, and a sagittal section of the segmentation is shown in&#160;Figure 2. For the purpose of illustrating extreme possible differences between manual and automatic tracings, slices of the AMY from a representative subject with erroneous automated segmentation were juxtapo...

Watch this Scientific Journal Video about A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures at JoVE.com

A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures

The present work provides a comprehensive set of guidelines for manually tracing the medial temporal lobe (MTL) structures. This protocol can be applied to research involving structural and/or combined structural-functional magnetic resonance imaging (MRI) investigations of the MTL, in both healthy and clinical groups.

The present paper describes a comprehensive protocol for manual tracing of the set of brain regions comprising the medial temporal lobe (MTL): amygdala, ...

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