FMRIB's Integrated Registration And Segmentation Tool Research Articles

Automated subcortical volume estimation from 2D MRI in epilepsy and implications for clinical trials

PurposeMost techniques used for automatic segmentation of subcortical brain regions are developed for three-dimensional (3D) MR images. MRIs obtained in non-specialist hospitals may be non-isotropic and two-dimensional (2D). Automatic segmentation of 2D images may be challenging and represents a lost opportunity to perform quantitative image analysis. We determine the performance of a modified subcortical segmentation technique applied to 2D images in patients with idiopathic generalised epilepsy (IGE).MethodsVolume estimates were derived from 2D (0.4 × 0.4 × 3 mm) and 3D (1 × 1x1mm) T1-weighted acquisitions in 31 patients with IGE and 39 healthy controls. 2D image segmentation was performed using a modified FSL FIRST (FMRIB Integrated Registration and Segmentation Tool) pipeline requiring additional image reorientation, cropping, interpolation and brain extraction prior to conventional FIRST segmentation. Consistency between segmentations was assessed using Dice coefficients and volumes across both approaches were compared between patients and controls. The influence of slice thickness on consistency was further assessed using 2D images with slice thickness increased to 6 mm.ResultsAll average Dice coefficients showed excellent agreement between 2 and 3D images across subcortical structures (0.86–0.96). Most 2D volumes were consistently slightly lower compared to 3D volumes. 2D images with increased slice thickness showed lower agreement with 3D images with lower Dice coefficients (0.55–0.83). Significant volume reduction of the left and right thalamus and putamen was observed in patients relative to controls across 2D and 3D images.ConclusionAutomated subcortical volume estimation of 2D images with a resolution of 0.4 × 0.4x3mm using a modified FIRST pipeline is consistent with volumes derived from 3D images, although this consistency decreases with an increased slice thickness. Thalamic and putamen atrophy has previously been reported in patients with IGE. Automated subcortical volume estimation from 2D images is feasible and most reliable at using in-plane acquisitions greater than 1 mm x 1 mm and provides an opportunity to perform quantitative image analysis studies in clinical trials.

Striatum Shape Hypertrophy in Early Stage Parkinson's Disease With Excessive Daytime Sleepiness.

IntroductionExcessive daytime sleepiness (EDS) is one of the common and burdensome non-motor symptoms of Parkinson’s disease (PD). However, the underlying neuropathology mechanism in PD patients with EDS (PD-EDS) remains unclear. The present study aims to delineate potential locations of structural alteration of subcortical regions in early stage and drug-naïve PD-EDS.MethodsThe study had 252 patients with PD and 92 matched healthy controls (HC). EDS was estimated with the Epworth Sleepiness Scale, with a cutoff of 10. Ultimately, 59 patients were considered as PD-EDS. The remaining 193 were PD patients without EDS (PD-nEDS). FMRIB’s Integrated Registration and Segmentation Tool (FIRST) was employed to assess the volumetric and surface alterations of subcortical nuclei in PD and PD-EDS.ResultsVolumetric analyses found no difference in the subcortical nucleus volume between PD and HC, or PD-EDS and PD-nEDS groups. The shape analyses revealed the local atrophic changes in bilateral caudate and right putamen in patients with PD. In addition, the hypertrophic changes were located in the right putamen and left pallidum in PD-EDS than in PD-nEDS.ConclusionOur findings revealed the regional hypertrophy of the striatum in PD-EDS. Our results indicate that local hypertrophic striatum would be a valuable early biomarker for detecting the alteration in PD-EDS. The shape analysis contributes valuable information when investigating PD-EDS.

Larger regional volume of the thalamus in diarrhea-predominant irritable bowel syndrome: a cross-sectional study.

As a relay center between the cerebral cortex and various subcortical brain areas, the thalamus is repeatedly associated with the dysfunction of brain-gut interaction in patients with irritable bowel syndrome (IBS). However, the regional morphological alterations of the thalamus in IBS are not well defined. We acquired structural magnetic resonance data from 34 patients with IBS and 34 demographically similar healthy subjects. Data processing was performed using FMRIB's Integrated Registration and Segmentation Tool (FIRST). Volumetric analysis and surface-based vertex analysis were both carried out to characterize the morphology of the thalamus and other subcortical structures. Our results suggested that the majority (31 cases) of the patients with IBS had diarrhea-predominant symptoms. Volumetric analysis revealed a larger normalized volume of the right thalamus and left caudate nucleus in patients with IBS than in healthy controls. Surface analysis indicated that the difference arose mainly from the laterodorsal nucleus of the right thalamus, and the body of the left caudate nucleus. In addition, patients with IBS had different hemispheric asymmetries of the thalamus (rightward) and caudate nucleus (leftward) from controls (leftward for the thalamus and rightward for the caudate nucleus). In general, our results indicated that patients with diarrhea-predominant IBS had enlarged thalamus and caudate nucleus volumes, as well as altered hemispheric asymmetries of these two structures, compared with healthy controls. The neuroimaging evidence of these structural alterations helps clarify the underlying pathophysiology of diarrhea-predominant IBS.

Striatal structure and its association with N-Acetylaspartate and glutamate in autism spectrum disorder and obsessive compulsive disorder

Autism spectrum disorders (ASD) and obsessive compulsive disorder (OCD) are often comorbid and are associated with changes in striatal volumes and N-Acetylaspartate (NAA) and glutamate levels. Here, we investigated the relation between dorsal striatal volume and NAA and glutamate levels. We additionally compared striatal volume and shape between ASD, OCD and controls. T1-weighted magnetic resonance (MR) images, proton spectra (1H-MRS) in the left striatum, and phenotypic information were collected from 54 children with ASD, 32 with OCD, and 56 controls (aged 8–13 years) in a four-site study. Dorsal striatal volume and shape were determined using the FMRIB integrated registration and segmentation tool (FIRST). Spectra were processed with Linear Combination Model. The relationship of left striatal volume with NAA and glutamate was investigated, and group comparisons were performed for NAA levels and for bilateral striatal volume and shape. NAA levels were lower in subjects with ASD compared with controls (t=2.86, p=0.005) and were associated with striatal volume (β=0.37, t=2.78, p=0.008). Glutamate levels were also associated with volume in the ASD group (β=0.38, t=2.46, p=0.018). No group differences were found for striatal volume or shape, but a post-hoc diagnosis-by-hemisphere interaction (F(2,129)=3.86, p=0.024) revealed greater asymmetry (right>left) in striatal volume for the disorder-groups compared with controls. Our findings show involvement of NAA and glutamate in striatal volume in ASD and suggest greater asymmetry in paediatric ASD and OCD compared with controls, pointing to overlapping subcortical abnormalities. The lower NAA in ASD reflects reduced neuronal integrity or impaired neuronal functioning.

An improved FSL-FIRST pipeline for subcortical gray matter segmentation to study abnormal brain anatomy using quantitative susceptibility mapping (QSM)

Accurate and robust segmentation of subcortical gray matter (SGM) nuclei is required in many neuroimaging applications. FMRIB's Integrated Registration and Segmentation Tool (FIRST) is one of the most popular software tools for automated subcortical segmentation based on T1-weighted (T1w) images. In this work, we demonstrate that FIRST tends to produce inaccurate SGM segmentation results in the case of abnormal brain anatomy, such as present in atrophied brains, due to a poor spatial match of the subcortical structures with the training data in the MNI space as well as due to insufficient contrast of SGM structures on T1w images. Consequently, such deviations from the average brain anatomy may introduce analysis bias in clinical studies, which may not always be obvious and potentially remain unidentified. To improve the segmentation of subcortical nuclei, we propose to use FIRST in combination with a special Hybrid image Contrast (HC) and Non-Linear (nl) registration module (HC-nlFIRST), where the hybrid image contrast is derived from T1w images and magnetic susceptibility maps to create subcortical contrast that is similar to that in the Montreal Neurological Institute (MNI) template. In our approach, a nonlinear registration replaces FIRST's default linear registration, yielding a more accurate alignment of the input data to the MNI template. We evaluated our method on 82 subjects with particularly abnormal brain anatomy, selected from a database of >2000 clinical cases. Qualitative and quantitative analyses revealed that HC-nlFIRST provides improved segmentation compared to the default FIRST method.

Measurement of Cortical Thickness and Volume of Subcortical Structures in Multiple Sclerosis: Agreement between 2D Spin-Echo and 3D MPRAGE T1-Weighted Images.

Gray matter pathology is known to occur in multiple sclerosis and is related to disease outcomes. FreeSurfer and the FMRIB Integrated Registration and Segmentation Tool (FIRST) have been developed for measuring cortical and subcortical gray matter in 3D-gradient-echo T1-weighted images. Unfortunately, most historical MS cohorts do not have 3D-gradient-echo, but 2D-spin-echo images instead. We aimed to evaluate whether cortical thickness and the volume of subcortical structures measured with FreeSurfer and FIRST could be reliably measured in 2D-spin-echo images and to investigate the strength and direction of clinicoradiologic correlations. Thirty-eight patients with MS and 2D-spin-echo and 3D-gradient-echo T1-weighted images obtained at the same time were analyzed by using FreeSurfer and FIRST. The intraclass correlation coefficient between the estimates was obtained. Correlation coefficients were used to investigate clinicoradiologic associations. Subcortical volumes obtained with both FreeSurfer and FIRST showed good agreement between 2D-spin-echo and 3D-gradient-echo images, with 68.8%-76.2% of the structures having either a substantial or almost perfect agreement. Nevertheless, with FIRST with 2D-spin-echo, 18% of patients had mis-segmentation. Cortical thickness had the lowest intraclass correlation coefficient values, with only 1 structure (1.4%) having substantial agreement. Disease duration and the Expanded Disability Status Scale showed a moderate correlation with most of the subcortical structures measured with 3D-gradient-echo images, but some correlations lost significance with 2D-spin-echo images, especially with FIRST. Cortical thickness estimates with FreeSurfer on 2D-spin-echo images are inaccurate. Subcortical volume estimates obtained with FreeSurfer and FIRST on 2D-spin-echo images seem to be reliable, with acceptable clinicoradiologic correlations for FreeSurfer.

Smaller Amygdala Volumes in Patients With Chronic Low Back Pain Compared With Healthy Control Individuals

Although preclinical and clinical data strongly support an association between the amygdala and chronic pain by the presence of mood and cognitive disturbances in affected individuals, little attention has been paid to morphometric measurement of the structure in patients with chronic low back pain (CLBP). In the present study, magnetic resonance volumetric and surface analysis, using FMRIB's integrated registration and segmentation tool (FIRST), were performed to compare structural magnetic resonance imaging data obtained from 33 patients with CLBP with those obtained from 33 demographically similar healthy control individuals. Our results indicated that the normalized volumes of the left and right amygdala were significantly smaller in the CLBP group than in the control group. Detailed surface analyses further localized these differences. The degree of volume reduction was different between the left and right amygdala, with a greater involvement of the left side. Both groups exhibited similar significant hemispheric asymmetry for the amygdala (left > right). Similar asymmetry was suggested in the subgroup of 24 unmedicated patients. No significant correlations were found between amygdala volumes and pain characteristics or depressive symptoms. Our study provides in vivo imaging evidence of abnormal morphology of the amygdala in patients with CLBP using a fully automated segmentation method. PerspectiveOur study found that patients with CLBP had statistically significantly smaller normalized volumes of the bilateral amygdala, compared with healthy control individuals, with a greater involvement of the left side. These results may help to characterize the impaired affective-cognitive dimension in patients with chronic pain.

Developmental sex differences in resting state functional connectivity of amygdala sub-regions

During adolescence, considerable social and biological changes occur that interact with functional brain maturation, some of which are sex-specific. The amygdala is one brain area that has displayed sexual dimorphism, specifically in socio-affective (superficial amygdala [SFA]), stress (centromedial amygdala [CMA]), and learning and memory (basolateral amygdala [BLA]) processing. The amygdala has also been implicated in mood and anxiety disorders which display sex-specific features, most prominently observed during adolescence. Using functional magnetic resonance imaging (fMRI), the present study examined the interaction of age and sex on resting state functional connectivity (RSFC) of amygdala sub-regions, BLA and SFA, in a sample of healthy adolescents between the ages 10 and 16years (n=122, 71 boys). Whole-brain, voxel-wise partial correlation analyses were conducted to determine RSFC of bilateral BLA and SFA seed regions, created using the Eickhoff–Zilles maximum probability maps based on cytoarchitectonic mapping and FMRIB's Integrated Registration and Segmentation Tool (FIRST). Monte Carlo simulation was implemented to correct for multiple comparisons (threshold of 53 contiguous voxels with a z-value≥2.25). Results indicated that with increasing age, there was a corresponding decrease in RSFC between both amygdala sub-regions and parieto-occipital cortices, with a concurrent increase in RSFC with medial prefrontal cortex (mPFC). Specifically, boys and girls demonstrated increased coupling of mPFC and left and right SFA with age, respectively; however, neither sex showed increased connectivity between mPFC and BLA, which could indicate relative immaturity of fronto-limbic networks that is similar across sex. A dissociation in connectivity between BLA- and SFA-parieto-occipital RSFC emerged, in which girls had weaker negative RSFC between SFA and parieto-occipital regions and boys had weaker negative RSFC of BLA and parieto-occipital regions with increased age, both standing in contrast to adult patterns of amygdala sub-regional RSFC. The present findings suggest relative immaturity of amygdala sub-regional RSFC with parieto-occipital cortices during adolescence, with unique patterns in both sexes that may support memory and socio-affective processing in boys and girls, respectively. Understanding the underlying normative functional architecture of brain networks associated with the amygdala during adolescence may better inform future research of the neural features associated with increased risk for internalizing psychopathology.

Contralesional Thalamic Surface Atrophy and Functional Disconnection 3 Months after Ischemic Stroke

Background: Remote structural and functional changes have been previously described after stroke and may have an impact on clinical outcome. We aimed to use multimodal MRI to investigate contralesional subcortical structural and functional changes 3 months after anterior circulation ischemic stroke. Methods: Fifteen patients with acute ischemic stroke had multimodal MRI imaging (including high resolution structural T1-MPRAGE and resting state fMRI) within 1 week of onset and at 1 and 3 months. Seven healthy controls of similar age group were also imaged at a single time point. Contralesional subcortical structural volume was assessed using an automated segmentation algorithm in FMRIB's Integrated Registration and Segmentation Tool (FIRST). Functional connectivity changes were assessed using the intrinsic connectivity contrast (ICC), which was calculated using the functional connectivity toolbox for correlated and anticorrelated networks (Conn). Results: Contralesional thalamic volume in the stroke patients was significantly reduced at 3 months compared to baseline (median change -2.1%, interquartile range [IQR] -3.4-0.4, p = 0.047), with the predominant areas demonstrating atrophy geometrically appearing to be the superior and inferior surface. The difference in volume between the contralesional thalamus at baseline (mean 6.41 ml, standard deviation [SD] 0.6 ml) and the mean volume of the 2 thalami in controls (mean 7.22 ml, SD 1.1 ml) was not statistically significant. The degree of longitudinal thalamic atrophy in patients was correlated with baseline stroke severity with more severe strokes being associated with a greater degree of atrophy (Spearman's rho -0.54, p = 0.037). There was no significant difference between baseline contralesional thalamic ICC in patients and control thalamic ICC. However, in patients, there was a significant linear reduction in the mean ICC of the contralesional thalamus over the imaging time points (p = 0.041), indicating reduced connectivity to the remainder of the brain. Conclusions: These findings highlight the importance of remote brain areas, such as the contralesional thalamus, in stroke recovery. Similar methods have the potential to be used in the prediction of stroke outcome or as imaging biomarkers of stroke recovery.

Subcortical brain segmentation of two dimensional T1-weighted data sets with FMRIB's Integrated Registration and Segmentation Tool (FIRST).

Brain atrophy has been identified as an important contributing factor to the development of disability in multiple sclerosis (MS). In this respect, more and more interest is focussing on the role of deep grey matter (DGM) areas. Novel data analysis pipelines are available for the automatic segmentation of DGM using three-dimensional (3D) MRI data. However, in clinical trials, often no such high-resolution data are acquired and hence no conclusions regarding the impact of new treatments on DGM atrophy were possible so far. In this work, we used FMRIB's Integrated Registration and Segmentation Tool (FIRST) to evaluate the possibility of segmenting DGM structures using standard two-dimensional (2D) T1-weighted MRI. In a cohort of 70 MS patients, both 2D and 3D T1-weighted data were acquired. The thalamus, putamen, pallidum, nucleus accumbens, and caudate nucleus were bilaterally segmented using FIRST. Volumes were calculated for each structure and for the sum of basal ganglia (BG) as well as for the total DGM. The accuracy and reliability of the 2D data segmentation were compared with the respective results of 3D segmentations using volume difference, volume overlap and intra-class correlation coefficients (ICCs). The mean differences for the individual substructures were between 1.3% (putamen) and −25.2% (nucleus accumbens). The respective values for the BG were −2.7% and for DGM 1.3%. Mean volume overlap was between 89.1% (thalamus) and 61.5% (nucleus accumbens); BG: 84.1%; DGM: 86.3%. Regarding ICC, all structures showed good agreement with the exception of the nucleus accumbens. The results of the segmentation were additionally validated through expert manual delineation of the caudate nucleus and putamen in a subset of the 3D data. In conclusion, we demonstrate that subcortical segmentation of 2D data are feasible using FIRST. The larger subcortical GM structures can be segmented with high consistency. This forms the basis for the application of FIRST in large 2D MRI data sets of clinical trials in order to determine the impact of therapeutic interventions on DGM atrophy in MS.

Reduced thalamic volumes in major depressive disorder

Altered function in the limbic–cortical–striatial–pallidal–thalamic (LCSPT) circuit has been implicated in the pathophysiology of major depressive disorder (MDD). This study evaluated volumetric differences in subcortical volumes between depressed subjects with MDD (N=142), subjects with MDD in remission (N=72), and healthy controls (N=169). Participants underwent magnetic resonance imaging (MRI) scanning, and subcortical volumes were extracted using FMRIB's Integrated Registration and Segmentation Tool (FIRST), University of Oxford, UK. The depressed MDD subjects exhibited significantly smaller volumes in the bilateral thalamus and hippocampus compared to control subjects, and the differences in the bilateral thalamus remained significant after controlling for total intracranial volume. In a smaller subset of healthy controls and depressed MDD subjects matched to the remitted MDD subjects, significant differences in volume were observed across groups in the bilateral thalamus, as well as the right lateralized caudate, hippocampus, and pallidum; these were primarily accounted for by differences between the depressed MDD subjects versus both the remitted and healthy subjects, though none of these changes remained significant after controlling for total intracranial volume (TIV). Volumetric reductions in the thalamus and hippocampus may contribute to dysfunction within subcortical–cortical networks, consistent with previous evidence of metabolic and hemodynamic abnormalities in these regions in MDD.

Reduced Hippocampal Volume in Healthy Young ApoE4 Carriers: An MRI Study

The E4 allele of the ApoE gene has consistently been shown to be related to an increased risk of Alzheimer's disease (AD). The E4 allele is also associated with functional and structural grey matter (GM) changes in healthy young, middle-aged and older subjects. Here, we assess volumes of deep grey matter structures of 22 healthy younger ApoE4 carriers and 22 non-carriers (20–38 years). Volumes of the nucleus accumbens, amygdala, caudate nucleus, hippocampus, pallidum, putamen, thalamus and brain stem were calculated by FMRIB's Integrated Registration and Segmentation Tool (FIRST) algorithm. A significant drop in volume was found in the right hippocampus of ApoE4 carriers (ApoE4+) relative to non-carriers (ApoE4−), while there was a borderline significant decrease in the volume of the left hippocampus of ApoE4 carriers. The volumes of no other structures were found to be significantly affected by genotype. Atrophy has been found to be a sensitive marker of neurodegenerative changes, and our results show that within a healthy young population, the presence of the ApoE4+ carrier gene leads to volume reduction in a structure that is vitally important for memory formation. Our results suggest that the hippocampus may be particularly vulnerable to further degeneration in ApoE4 carriers as they enter middle and old age. Although volume reductions were noted bilaterally in the hippocampus, atrophy was more pronounced in the right hippocampus. This finding relates to previous work which has noted a compensatory increase in right hemisphere activity in ApoE4 carriers in response to preclinical declines in memory function. Possession of the ApoE4 allele may lead to greater predilection for right hemisphere atrophy even in healthy young subjects in their twenties.

Association between subcortical volumes and verbal memory in unmedicated depressed patients and healthy controls

Research has shown poor performance on verbal memory tasks in patients with major depressive disorder relative to healthy controls, as well as structural abnormalities in the subcortical structures that form the limbic-cortical-striatal-pallidal-thalamic circuitry. Few studies, however, have attempted to link the impairments in learning and memory in depression with these structural abnormalities, and of those which have done so, most have included patients medicated with psychotropic agents likely to influence cognitive performance. This study thus examines the relationship between subcortical structural abnormalities and verbal memory using the California Verbal Learning Test (CVLT) in unmedicated depressed patients. A T1 weighted magnetic resonance imaging scan and the CVLT were obtained on 45 subjects with major depressive disorder and 44 healthy controls. Using the FMRIB's Integrated Registration and Segmentation Tool (FIRST) volumes of selected subcortical structures were segmented and correlated with CVLT performance. Depressed participants showed significantly smaller right thalamus and right hippocampus volumes than healthy controls. Depressed participants also showed impaired performance on global verbal learning ability, and appeared to depend upon an inferior memory strategy (serial clustering). Measures of serial clustering were correlated significantly with right hippocampal volumes in depressed participants. Our findings indicate that depressed participants and healthy controls differ in the memory strategies they employ, and that while depressed participants had a smaller hippocampal volume, there was a positive correlation between volume and use of an inferior memory strategy. This suggests that larger hippocampal volume is related to better memory recall in depression, but specifically with regard to utilizing an inferior memory strategy.

SU-E-J-108: Quantitative Analysis of Longitudinal Cognitive Impairment Due to Radiation Therapy Based on Automatic Segmentation of Hippocampus and Subcortical Structure.

In this study, we developed a quantitative analysis tool based on patient's longitudinal MR images to 1) measure the radiation dose received by each subcortical structure, 2) follow the change of volume and shape of each structure longitudinally. This tool provides a systematic approach to study the radiation therapy (and subsequent chemotherapy) associated with cognitive impairments. MRI scans of one patient taken before and after radiation therapy are demonstrated in this study. 3D Conformal radiation therapy was performed on RapidArc™. An open source MRI analysis tool, FMRIB's Integrated Registration and Segmentation Tool (FIRST), was used for segmentation. The images are registered to a standard template with expert-defined labeling for all sub-cortical structures, and the labeling of each structure is mapped back to the individual MRI space for segmentation. After the segmentation, the radiation dose map was coregistered to the MRI space to calculate the dose received by each structure. For the structure that is contained within the radiation zone, we can calculate the total dose based on the volumetric distribution of radiation dose. For the structure that is outside the radiation field, we can calculate the distance from the radiation zone. We have demonstrated in this work that the analysis can be done for all segmented sub-cortical structures. The change of volume before and after radiation treatment can be analyzed, and the results can be correlated with the change of cognitive performance over time. We presented an automated tool for efficient, quantitative and user-independent measurements of radiation dose in subcortical structures. The obtained results can be correlated with the cognitive test score and the clinical outcome to evaluate radiation and the subsequent chemotherapy induced changes in brain structures and functions.

Strongly reduced volumes of putamen and thalamus in Alzheimer's disease: an MRI study

Atrophy is regarded a sensitive marker of neurodegenerative pathology. In addition to confirming the well-known presence of decreased global grey matter and hippocampal volumes in Alzheimer's disease, this study investigated whether deep grey matter structure also suffer degeneration in Alzheimer's disease, and whether such degeneration is associated with cognitive deterioration. In this cross-sectional correlation study, two groups were compared on volumes of seven subcortical regions: 70 memory complainers (MCs) and 69 subjects diagnosed with probable Alzheimer's disease. Using 3T 3D T1 MR images, volumes of nucleus accumbens, amygdala, caudate nucleus, hippocampus, pallidum, putamen and thalamus were automatically calculated by the FMRIB's Integrated Registration and Segmentation Tool (FIRST)—algorithm FMRIB's Software Library (FSL). Subsequently, the volumes of the different regions were correlated with cognitive test results. In addition to finding the expected association between hippocampal atrophy and cognitive decline in Alzheimer's disease, volumes of putamen and thalamus were significantly reduced in patients diagnosed with probable Alzheimer's disease. We also found that the decrease in volume correlated linearly with impaired global cognitive performance. These findings strongly suggest that, beside neo-cortical atrophy, deep grey matter structures in Alzheimer's disease suffer atrophy as well and that degenerative processes in the putamen and thalamus, like the hippocampus, may contribute to cognitive decline in Alzheimer's disease.