MR-based automatic delineation of volumes of interest in human brain PET images using probability maps

Svarer, Claus; Madsen, Karine; Hasselbalch, Steen G.; Pinborg, Lars H.; Haugbøl, Steven; Frøkjær, Vibe G.; Holm, Søren; Paulson, Olaf B.; Knudsen, Gitte M.

doi:10.1016/j.neuroimage.2004.10.017

Cited by 332 publications

(269 citation statements)

References 22 publications

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“…Volumes of interest (VOIs) were automatically delineated on each subject's MR image in a user-independent fashion with the Pvelab software package (freely available on www.nru.dk/downloads) (Svarer et al, 2005). For each of the 10-template VOI sets, a 12-parameter affine transformation and a warping field were calculated between the template MR image and the individual MR image for a subject.…”

Section: Voi Analysismentioning

confidence: 99%

“…The neocortical region consisted of a volume-weighted average of the following 8 cortical regions: Orbitofrontal cortex, medial inferior frontal cortex, superior frontal cortex, superior temporal cortex, medial inferior temporal cortex, sensory motor cortex, parietal cortex, and occipital cortex. The delineation of all VOIs except the midbrain have been described previously (Svarer et al, 2005). Midbrain was defined in the ACPC plane (the plane of the anterior and posterior commissure) as the superior limit and the boarder between the inferior colliculi and the superior cerebellar peduncle as the inferior limit.…”

Section: Voi Analysismentioning

confidence: 99%

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Cerebral serotonin transporter binding is inversely related to body mass index

et al. 2010

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Section: Voi Analysismentioning

confidence: 99%

Section: Voi Analysismentioning

confidence: 99%

Cerebral serotonin transporter binding is inversely related to body mass index

et al. 2010

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“…The data were analysed using a probability-map-based automatic delineation of 35 ROIs that delineates the whole brain (bilateral areas were counted as one ROI). 26 This method is a fast, objective, reproducible, and safe way to assess regional brain values from PET or SPECT scans, which has previously been described and validated. 26 The 35 ROIs are based on manual definition of these ROIs in MRI images of 10 healthy controls.…”

Section: Magnetic Resonance Imagingmentioning

confidence: 99%

“…26 This method is a fast, objective, reproducible, and safe way to assess regional brain values from PET or SPECT scans, which has previously been described and validated. 26 The 35 ROIs are based on manual definition of these ROIs in MRI images of 10 healthy controls. Each ROI represents the volume that is present in each individual ROI after warping to a standard brain.…”

Section: Magnetic Resonance Imagingmentioning

confidence: 99%

Reduced GABAA benzodiazepine receptor binding in veterans with post-traumatic stress disorder

et al. 2007

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c-Aminobutyric acid (GABA A ) receptors are thought to play an important role in modulating the central nervous system in response to stress. Animal data have shown alterations in the GABA A receptor complex by uncontrollable stressors. SPECT imaging with benzodiazepine ligands showed lower distribution volumes of the benzodiazepine-GABA A receptor in the prefrontal cortex of patients with post-traumatic stress disorder (PTSD) in one, but not in another study. The objective of the present study was to assess differences in the benzodiazepine-GABA A receptor complex in veterans with and without PTSD using [ 11 C]flumazenil and positron emission tomography (PET). Nine drug naive male Dutch veterans with deployment related PTSD and seven male Dutch veterans without PTSD were recruited, and matched for age, region and year of deployment. Each subject received a [ 11 C]flumazenil PET scan and a structural magnetic resonance imaging scan. Dynamic 3D PET scans with a total duration of 60 min were acquired, and binding in template based and manually defined regions of interest (ROI) was quantified using validated plasma input and reference tissue models. In addition, parametric binding potential images were compared on a voxel-by-voxel basis using statistical parametric mapping (SPM2). ROI analyses using both template based and manual ROIs showed significantly reduced [ 11 C]flumazenil binding in PTSD subjects throughout the cortex, hippocampus and thalamus. SPM analysis confirmed these results. The observed global reduction of [ 11 C]flumazenil binding in patients with PTSD provides circumstantial evidence for the role of the benzodiazepine-GABA A receptor in the pathophysiology of PTSD and is consistent with previous animal research and clinical psychopharmacological studies.

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“…However, issues such as tissue inhomogeneity, weakly-defined boundaries, or high variability between subjects present challenges for gray-scale registration methods alone, thus incorporating additional constraints such as corresponding landmarks can help to initialize the computation of matching transformation. It should be noted that several deformable-template methods exist which do not require landmark placement; in particular, Svarer et al (2005) and Heckemann et al (2006) segment subcortical structures with a high level of accuracy using multiple atlas propagation and label fusion.…”

mentioning

confidence: 99%

FreeSurfer-initiated fully-automated subcortical brain segmentation in MRI using Large Deformation Diffeomorphic Metric Mapping

Wang²,

2008

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Fully-automated brain segmentation methods have not been widely adopted for clinical use because of issues related to reliability, accuracy, and limitations of delineation protocol. By combining the probabilistic-based FreeSurfer (FS) method with the Large Deformation Diffeomorphic Metric Mapping (LDDMM) based label propagation method, we are able to increase reliability and accuracy, and allow for flexibility in template choice. Our method uses the automated FreeSurfer subcortical labeling to provide a coarse to fine introduction of information in the LDDMM template-based segmentation resulting in a fully-automated subcortical brain segmentation method (FS+LDDMM).One major advantage of the FS+LDDMM-based approach is that the automatically generated segmentations generated are inherently smooth, thus subsequent steps in shape analysis can directly follow without manual post-processing or loss of detail.We have evaluated our new FS+LDDMM method on several databases containing a total of 50 subjects with different pathologies, scan sequences and manual delineation protocols for labeling the basal ganglia, thalamus, and hippocampus. In healthy controls we report Dice overlap measures of 0. 81, 0.83, 0.74, 0.86 and 0.75 for the right caudate nucleus, putamen, pallidum, thalamus and hippocampus respectively. We also find statistically significant improvement of accuracy in FS +LDDMM over FreeSurfer for the caudate nucleus and putamen of Huntington's disease and Tourette's syndrome subjects, and the right hippocampus of Schizophrenia subjects.

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MR-based automatic delineation of volumes of interest in human brain PET images using probability maps

Cited by 332 publications

References 22 publications

Cerebral serotonin transporter binding is inversely related to body mass index

Cerebral serotonin transporter binding is inversely related to body mass index

Reduced GABAA benzodiazepine receptor binding in veterans with post-traumatic stress disorder

FreeSurfer-initiated fully-automated subcortical brain segmentation in MRI using Large Deformation Diffeomorphic Metric Mapping

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