Dataset Information

Recommendations for Processing Head CT Data.

ABSTRACT: Many research applications of neuroimaging use magnetic resonance imaging (MRI). As such, recommendations for image analysis and standardized imaging pipelines exist. Clinical imaging, however, relies heavily on X-ray computed tomography (CT) scans for diagnosis and prognosis. Currently, there is only one image processing pipeline for head CT, which focuses mainly on head CT data with lesions. We present tools and a complete pipeline for processing CT data, focusing on open-source solutions, that focus on head CT but are applicable to most CT analyses. We describe going from raw DICOM data to a spatially normalized brain within CT presenting a full example with code. Overall, we recommend anonymizing data with Clinical Trials Processor, converting DICOM data to NIfTI using dcm2niix, using BET for brain extraction, and registration using a publicly-available CT template for analysis.

SUBMITTER: Muschelli J

PROVIDER: S-EPMC6738271 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Recommendations for Processing Head CT Data.

Muschelli John J

Frontiers in neuroinformatics 20190904

Many research applications of neuroimaging use magnetic resonance imaging (MRI). As such, recommendations for image analysis and standardized imaging pipelines exist. Clinical imaging, however, relies heavily on X-ray computed tomography (CT) scans for diagnosis and prognosis. Currently, there is only one image processing pipeline for head CT, which focuses mainly on head CT data with lesions. We present tools and a complete pipeline for processing CT data, focusing on open-source solutions, tha ...[more]

PMID: 31551745

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Project description:BackgroundSpectral CT material decomposition provides quantitative information but is challenged by the instability of the inversion into basis materials. We have previously proposed the constrained One-Step Spectral CT Image Reconstruction (cOSSCIR) algorithm to stabilize the material decomposition inversion by directly estimating basis material images from spectral CT data. cOSSCIR was previously investigated on phantom data.PurposeThis study investigates the performance of cOSSCIR using head CT datasets acquired on a clinical photon-counting CT (PCCT) prototype. This is the first investigation of cOSSCIR for large-scale, anatomically complex, clinical PCCT data. The cOSSCIR decomposition is preceded by a spectrum estimation and nonlinear counts correction calibration step to address nonideal detector effects.MethodsHead CT data were acquired on an early prototype clinical PCCT system using an edge-on silicon detector with eight energy bins. Calibration data of a step wedge phantom were also acquired and used to train a spectral model to account for the source spectrum and detector spectral response, and also to train a nonlinear counts correction model to account for pulse pileup effects. The cOSSCIR algorithm optimized the bone and adipose basis images directly from the photon counts data, while placing a grouped total variation (TV) constraint on the basis images. For comparison, basis images were also reconstructed by a two-step projection-domain approach of Maximum Likelihood Estimation (MLE) for decomposing basis sinograms, followed by filtered backprojection (MLE + FBP) or a TV minimization algorithm (MLE + TVmin ) to reconstruct basis images. We hypothesize that the cOSSCIR approach will provide a more stable inversion into basis images compared to two-step approaches. To investigate this hypothesis, the noise standard deviation in bone and soft-tissue regions of interest (ROIs) in the reconstructed images were compared between cOSSCIR and the two-step methods for a range of regularization constraint settings.ResultscOSSCIR reduced the noise standard deviation in the basis images by a factor of two to six compared to that of MLE + TVmin , when both algorithms were constrained to produce images with the same TV. The cOSSCIR images demonstrated qualitatively improved spatial resolution and depiction of fine anatomical detail. The MLE + TVmin algorithm resulted in lower noise standard deviation than cOSSCIR for the virtual monoenergetic images (VMIs) at higher energy levels and constraint settings, while the cOSSCIR VMIs resulted in lower noise standard deviation at lower energy levels and overall higher qualitative spatial resolution. There were no statistically significant differences in the mean values within the bone region of images reconstructed by the studied algorithms. There were statistically significant differences in the mean values within the soft-tissue region of the reconstructed images, with cOSSCIR producing mean values closer to the expected values.ConclusionsThe cOSSCIR algorithm, combined with our previously proposed spectral model estimation and nonlinear counts correction method, successfully estimated bone and adipose basis images from high resolution, large-scale patient data from a clinical PCCT prototype. The cOSSCIR basis images were able to depict fine anatomical details with a factor of two to six reduction in noise standard deviation compared to that of the MLE + TVmin two-step approach.

Project description:ObjectivesThe aim of this study was to evaluate whether simple 2D measurements in axial slices of head and neck CT examinations correlate with generally established measurements of body composition in abdominal CT at the height of the third lumbar vertebra and thus allow for an estimation of muscle and fat masses.MethodsOne hundred twenty-two patients who underwent concurrent CT of the head and neck and the abdomen between July 2016 and July 2020 were retrospectively included. For a subset of 30 patients, additional bioelectrical impedance analysis (BIA) was available. Areas of paraspinal muscles at the height of the third (C3) and fifth cervical vertebrae (C5) as well as the total cross-sectional area at the height of C3 and at the submandibular level were correlated with the results of abdominal measurements and BIA. Furthermore, intra- and interreader variabilities of all measurements were assessed.ResultsRegarding adipose tissue, good correlations were found between the total cross-sectional area of the patient's body at the submandibular level and at the height of C3 between both abdominal measurements and BIA results (r = 0.8-0.92; all p < 0.001). Regarding muscle, the total paraspinal muscle area at the height of C3 and C5 showed strong correlations with abdominal measurements and moderate to strong correlations with BIA results (r = 0.44-0.80; all p < 0.001), with the muscle area on C5 yielding slightly higher correlations.ConclusionsBody composition information can be obtained with comparable reliability from head and neck CT using simple biplanar measurements as from abdominal CT.Key points• The total paraspinal muscle area at the height of C3 and C5 correlates strongly with abdominal muscle mass. • The total cross-sectional area at the submandibular level and at the height of C3 shows good correlations with abdominal fat mass. • The described measurements facilitate a rapid, opportunistic assessment of relevant body composition parameters.

Dataset Information

Recommendations for Processing Head CT Data.

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Recommendations for Processing Head CT Data.

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