Biology subjects

Craddock, R. C.

Publications and source records attributed to Craddock, R. C..

4 recordsLinked to original sources

bioRxiv2017

The Anatomical Tracings of Lesions After Stroke (ATLAS) Dataset - Release 1.1

Stroke is the leading cause of adult disability worldwide, with up to two-thirds of individuals experiencing long-term disabilities. Large-scale neuroimaging studies have shown promise in identifying robust biomarkers (e.g., measures of brain structure) of long-term stroke recovery following rehabilitation. However, analyzing large rehabilitation-related datasets is problematic due to barriers in accurate stroke lesion segmentation. Manually-traced lesions are currently the gold standard for lesion segmentation on T1-weighted MRIs, but are labor intensive and require anatomical expertise. While algorithms have been developed to automate this process, the results often lack accuracy. Newer algorithms that employ machine-learning techniques are promising, yet these require large training datasets to optimize performance. Here we present ATLAS (Anatomical Tracings of Lesions After Stroke), an open-source dataset of 304 T1-weighted MRIs with manually segmented lesions and metadata. This large, diverse dataset can be used to train and test lesion segmentation algorithms and provides a standardized dataset for comparing the performance of different segmentation methods. We hope ATLAS release 1.1 will be a useful resource to assess and improve the accuracy of current lesion segmentation methods.

neuroscience↗

bioRxiv2017

Data-driven Assessment of Structural Image Quality

Data quality is increasingly recognized as one of the most important confounding factors in brain imaging research. It is particularly important for studies of brain development, where age is systematically related to in-scanner motion and data quality. Prior work has demonstrated that in-scanner head motion biases estimates of structural neuroimaging measures. However, objective measures of data quality are not available for most structural brain images. Here we sought to identify quantitative measures of data quality for T1-weighted volumes, describe how such measures of quality relate to cortical thickness, and delineate how this in turn may bias inference regarding associations with age in youth. Three highly-trained raters provided manual ratings of 1,840 raw T1-weighted volumes. These images included a training set of 1,065 images from Philadelphia Neurodevelopmental Cohort (PNC), a test set of 533 images from the PNC, as well as an external test set of 242 adults acquired on a different scanner. Manual ratings were compared to automated quality measures provided by the Preprocessed Connectomes Projects Quality Assurance Protocol (QAP), as well as FreeSurfers Euler number, which summarizes the topological complexity of the reconstructed cortical surface. Results revealed that the Euler number was consistently correlated with manual ratings across samples. Furthermore, the Euler number could be used to identify images scored \"unusable\" by human raters with a high degree of accuracy (AUC: 0.98-0.99), and outperformed proxy measures from functional timeseries acquired in the same scanning session. The Euler number also was significantly related to cortical thickness in a regionally heterogeneous pattern that was consistent across datasets and replicated prior results. Finally, data quality both inflated and obscured associations with age during adolescence. Taken together, these results indicate that reliable measures of data quality can be automatically derived from T1-weighted volumes, and that failing to control for data quality can systematically bias the results of studies of brain maturation.

bioinformatics↗

bioRxiv2016

Predicting brain-age from multimodal imaging data captures cognitive impairment

The disparity between the chronological age of an individual and their brain-age measured based on biological information has the potential to offer clinically-relevant biomarkers of neurological syndromes that emerge late in the lifespan. While prior brain-age prediction studies have relied exclusively on either structural or functional brain data, here we investigate how multimodal brainimaging data improves age prediction. Using cortical anatomy and whole-brain functional connectivity on a large adult lifespan sample (N = 2354, age 19-82), we found that multimodal data improves brain-based age prediction, resulting in a mean absolute prediction error of 4.29 years. Furthermore, we found that the discrepancy between predicted age and chronological age captures cognitive impairment. Importantly, the brain-age measure was robust to confounding effects: head motion did not drive brain-based age prediction and our models generalized reasonably to an independent dataset acquired at a different site (N = 475). Generalization performance was increased by training models on a larger and more heterogeneous dataset. The robustness of multimodal brain-age prediction to confounds, generalizability across sites, and sensitivity to clinically-relevant impairments, suggests promising future application to the early prediction of neurocognitive disorders.\n\nHighlightsO_LIBrain-based age prediction is improved with multimodal neuroimaging data.\nC_LIO_LIParticipants with cognitive impairment show increased brain aging.\nC_LIO_LIAge prediction models are robust to motion and generalize to independent datasets from other sites.\nC_LI

neuroscience↗

bioRxiv2016

Individual differences in functional connectivity during naturalistic viewing conditions

Naturalistic viewing paradigms such as movies have been shown to reduce participant head motion and improve arousal during fMRI scanning relative to task-free rest, and have been used to study both functional connectivity and task-evoked BOLD-signal changes. These task-evoked changes result in cortical activity that is synchronized across subjects and involves large areas of the cortex, and it is unclear whether individual differences in functional connectivity are enhanced or diminished under such naturalistic conditions. This work first aims to characterize variability in functional connectivity (FC) across two distinct movie conditions and eyes-open rest (n=34 healthy adults, 2 scan sessions each). At the whole-brain level, we found that movies have higher intra- and inter-subject correlations in cluster-wise FC relative to rest. The anatomical distribution of inter-subject variability was similar across conditions, with higher variability occurring at the lateral prefrontal lobes and temporoparietal junctions. Second, we used an unsupervised test-retest matching (or \"finger-printin\") algorithm that identifies individual subjects from within a group based on functional connectivity patterns, quantifying the accuracy of the algorithm across the three conditions. We also evaluated the impact of parcellation resolution, scan duration, and number of edges on observed inter-individual differences. The movies and resting state all enabled identification of individual subjects based on FC matrices, with accuracies between 62 and 100%. Overall, pairings involving movies outperformed rest, and the more social and faster-paced movie attained 100% accuracy. When the parcellation resolution, scan duration and number of edges used were increased, accuracies improved across conditions, and the pattern of movies>rest was preserved. These results suggest that using dynamic stimuli such as movies enhances the detection of FC patterns that are distinct at the individual level.\n\nHighlightsO_LIIntra- and inter-subject FC correlations are compared across rest and movies.\nC_LIO_LIMovies outperformed rest in an unsupervised identification algorithm based on FC.\nC_LIO_LIMovies outperform rest regardless of parcellation, scan length, or number of edges.\nC_LIO_LIWatching movies enhances the detection of individual differences in FC.\nC_LI

neuroscience↗