Whole-head segmentation from Magnetic Resonance Images (MRI) establishes the foundation for individualized computational models using finite element method (FEM). This foundation paves the path for computer-aided solutions in fields such as non-invasive brain stimulation. Most current automatic head segmentation tools are developed using healthy young adults. Thus, they may neglect the older population that is more prone to age-related structural decline such as brain atrophy. In this work, we present a new deep learning method called GRACE, which stands for General, Rapid, And Comprehensive whole-hEad tissue segmentation. GRACE is trained and validated on a novel dataset that consists of 177 manually corrected MR-derived reference segmentations that have undergone meticulous manual review. Each T1-weighted MRI volume is segmented into 11 tissue types, including white matter, grey matter, eyes, cerebrospinal fluid, air, blood vessel, cancellous bone, cortical bone, skin, fat, and muscle. To the best of our knowledge, this work contains the largest manually corrected dataset to date in terms of number of MRIs and segmented tissues. GRACE outperforms five freely available software tools and a traditional 3D U-Net on a five-tissue segmentation task. On this task, GRACE achieves an average Hausdorff Distance of 0.21, which exceeds the runner-up at an average Hausdorff Distance of 0.36. GRACE can segment a whole-head MRI in about 3 seconds, while the fastest software tool takes about 3 minutes. In summary, GRACE segments a spectrum of tissue types from older adults’ T1-MRI scans at favorable accuracy and speed. The trained GRACE model is optimized on older adult heads to enable high-precision modeling in age-related brain disorders. To support open science, the GRACE code and trained weights are made available online and open to the research community at https://github.com/lab-smile/GRACE.
- NSF-PAR ID:
- 10350677
- Date Published:
- Journal Name:
- Journal of Neural Engineering
- Volume:
- 19
- Issue:
- 2
- ISSN:
- 1741-2560
- Page Range / eLocation ID:
- 026022
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract -
Recent shifts in the understanding of how the mind and brain retain information in working memory (WM) call for revision to traditional theories. Evidence of dynamic, “activity-silent,” short-term retention processes diverges from conventional models positing that information is always retained in WM by sustained neural activity in buffers. Such evidence comes from machine-learning methods that can decode patterns of brain activity and the simultaneous administration of transcranial magnetic stimulation (TMS) to causally manipulate brain activity in specific areas and time points. TMS can “ping” brain areas to both reactivate latent representations retained in WM and affect memory performance. On the basis of these findings, I argue for a supplement to sustained retention mechanisms. Brain-decoding methods also reveal that dynamic levels of representational codes are retained in WM, and these vary according to task context, from perceptual (sensory) codes in posterior areas to abstract, recoded representations distributed across frontoparietal regions. A dynamic-processing model of WM is advanced to account for the overall pattern of results.more » « less
-
more » « less
In this paper we propose a novel neurostimulation protocol that provides an intervention-based assessment to distinguish the contributions of different motor control networks in the cortico-spinal system. Specifically, we use a combination of non-invasive brain stimulation and neuromuscular stimulation to probe neuromuscular system behavior with targeted impulse-response system identification. In this protocol, we use an in-house developed human-machine interface (HMI) for an isotonic wrist movement task, where the user controls a cursor on-screen. During the task, we generate unique motor evoked potentials based on triggered cortical or spinal level perturbations. Externally applied brain-level perturbations are triggered through TMS to cause wrist flexion/extension during the volitional task. The resultant contraction output and related reflex responses are measured by the HMI. These movements also include neuromodulation in the excitability of the brain-muscle pathway via transcranial direct current stimulation. Colloquially, spinal-level perturbations are triggered through skin-surface neuromuscular stimulation of the wrist muscles. The resultant brain-muscle and spinal-muscle pathways perturbed by the TMS and NMES, respectively, demonstrate temporal and spatial differences as manifested through the human-machine interface. This then provides a template to measure the specific neural outcomes of the movement tasks, and in decoding differences in the contribution of cortical- (long-latency) and spinal-level (short-latency) motor control. This protocol is part of the development of a diagnostic tool that can be used to better understand how interaction between cortical and spinal motor centers changes with learning, or injury such as that experienced following stroke.
-
Transcranial magnetic stimulation (TMS) is widely used for noninvasive brain stimulation. However, existing TMS tools cannot deliver targeted neural stimulation to deep brain regions, even though many important neurological disorders originate from there. To design TMS tools capable of delivering deep and focused stimulation, we have developed both electric and magnetic field probes to evaluate and improve new designs and calibrate products. Previous works related to magnetic field measurement had no detailed description of probe design or optimization. In this work, we demonstrated a magnetic field probe made of a cylindrical inductor and an electrical field probe modified from Rogowski coil structure. Both have much smaller size and higher directivity than commercial dipole probes. Using probe, we can calibrate and monitor any new types of TMS coil or array design and verify measured results with the other probe. We mathematically analyze their characteristics and performance and obtained a two-dimensional vector plot of the induced electric field, which matched the measured results from the second type of probe. A commercial circular coil and a figure-8 coil, with relatively complex vector field distribution, were used as examples to demonstrate the high-resolution and accurate measurement capability of our probes.more » « less
-
Medical image segmentation is one of the most challenging tasks in medical image analysis and has been widely developed for many clinical applications. Most of the existing metrics have been first designed for natural images and then extended to medical images. While object surface plays an important role in medical segmentation and quantitative analysis i.e. analyze brain tumor surface, measure gray matter volume, most of the existing metrics are limited when it comes to analyzing the object surface, especially to tell about surface smoothness or roughness of a given volumetric object or to analyze the topological errors. In this paper, we first analysis both pros and cons of all existing medical image segmentation metrics, specially on volumetric data. We then propose an appropriate roughness index and roughness distance for medical image segmentation analysis and evaluation. Our proposed method addresses two kinds of segmentation errors, i.e. (i) topological errors on boundary/surface and (ii) irregularities on the boundary/surface. The contribution of this work is four-fold: (i) detect irregular spikes/holes on a surface, (ii) propose roughness index to measure surface roughness of a given object, (iii) propose a roughness distance to measure the distance of two boundaries/surfaces by utilizing the proposed roughness index and (iv) suggest an algorithm which helps to remove the irregular spikes/holes to smooth the surface. Our proposed roughness index and roughness distance are built upon the solid surface roughness parameter which has been successfully developed in the civil engineering.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1088/1741-2552/ac5586
