Jolinda Smith

Chronically Deafferented Sensory Cortex Recovers a Grossly Typical Organization after Allogenic Hand Transplantation

Amputation induces substantial reorganization of the body part somatotopy in primary sensory cortex (S1 complex, hereafter S1) [1, 2], and these effects of deafferentiation increase with time [3]. Determining whether these changes are reversible is critical for understanding the potential to recover from deafferenting injuries. Earlier BOLD fMRI data demonstrate increased S1 activity in response to stimulation of an allogenically transplanted hand [4]. Here, we report the first evidence that the representation of a transplanted hand can actually recapture the pre-amputation S1 hand territory. A 54-year-old male received a unilateral hand transplant 35 years after traumatic amputation of his right hand. Despite limited sensation, palmar tactile stimulation delivered 4 months post-transplant evoked contralateral S1 responses that were indistinguishable in location and amplitude from those detected in healthy matched controls. We find no evidence for persistent intrusion of representations of the face within the representation of the transplanted hand, although such intrusions are commonly reported in amputees [5, 6]. Our results suggest that even decades after complete deafferentiation, restoring afferent input to S1 leads to re-establishment of the gross hand representation within its original territory. Unexpectedly, large ipsilateral S1 responses accompanied sensory stimulation of the patients intact hand. These may reflect a change in interhemispheric inhibition that could contribute to maintaining latent hand representations during the period of amputation.

The first step for neuroimaging data analysis: DICOM to NIfTI conversion

BACKGROUND Clinical imaging data are typically stored and transferred in the DICOM format, whereas the NIfTI format has been widely adopted by scientists in the neuroimaging community. Therefore, a vital initial step in processing the data is to convert images from the complicated DICOM format to the much simpler NIfTI format. While there are a number of tools that usually handle DICOM to NIfTI conversion seamlessly, some variations can disrupt this process. NEW METHOD We provide some insight into the challenges faced with image conversion. First, different manufacturers implement the DICOM format differently which complicates the conversion. Second, different modalities and sub-modalities may need special treatment during conversion. Lastly, the image transferring and archiving can also impact the DICOM conversion. RESULTS We present results in several error-prone domains, including the slice order for functional imaging, phase encoding direction for distortion correction, effect of diffusion gradient direction, and effect of gantry correction for some imaging modality. COMPARISON WITH EXISTING METHODS Conversion tools are often designed for a specific manufacturer or modality. The tools and insight we present here are aimed at different manufacturers or modalities. CONCLUSIONS The imaging conversion is complicated by the variation of images. An understanding of the conversion basics can be helpful for identifying the source of the error. Here we provide users with simple methods for detecting and correcting problems. This also serves as an overview for developers who wish to either develop their own tools or adapt the open source tools created by the authors.

Former Hand Territory Activity Increases After Amputation During Intact Hand Movements, but Is Unaffected by Illusory Visual Feedback:

Background. In healthy adults, hand movements are controlled largely by the contralateral primary motor cortex. Following amputation, however, movements of the intact hand are accompanied by increased activity in the sensorimotor cortices of both cerebral hemispheres. Objective. The authors tested whether use of the intact hand reactivates the cortical territory formerly devoted to the now missing hand and whether these effects can be augmented by motor imagery (MI) and/or exposure to illusory visual “feedback” (VF) of the absent hand created with a mirror. Methods. Functional magnetic resonance imaging (fMRI) was used to delineate the boundaries of normative sensorimotor hand representations in healthy controls. Brain activity from 11 unilateral hand amputees was recorded while they performed aurally paced thumb–finger sequencing movements with their intact hands under 4 conditions: (1) motor execution of the intact hand alone (ME), (2) ME with corresponding MI of the amputated hand, (3) ME with VF of the amputated hand, and (4) ME with MI and VF. Results. Intact hand movements increased activity specifically within the former sensorimotor hand territory during all conditions, an effect that may be attributable to decreased levels of interhemispheric inhibition and/or use-dependent functional reorganization following amputation. This effect was not significantly increased by the addition of VF and/or MI of the amputated hand. However, in amputees, MI was associated with an expansion of this ipsilateral response into parietal, premotor, and presupplementary motor areas. Conclusion. Active engagement of the intact hand may be critical for therapies seeking to stimulate the former hand territory.

Towards a microcoil for intracranial and intraductal MR microscopy

Implantable RF-coils have enabled sub-mm resolution magnetic resonance images (MRI) of deep structures. Scaling down the size of RF coils has similarly provided a gain in signal-to-noise ratio in nuclear-magnetic-resonance spectroscopy. By combining both approaches we designed, fabricated, and imaged with an implantable microcoil catheter. While typical implantable catheters use a transverse magneti-zation, the axial magnetization of the microcoil provides improved sensitivity and allows visualization of the tissue beyond the distal end of the catheter. The microcoil catheter was designed with a diameter of 1 mm for future integration with intracranial devices, and for intraductal use in breast oncology. We modified the NMR-microcoil design to allow implantation of the RF coil, by winding the microcoil on medical-grade silicone tubing and incorporating leads on the catheter to connect circuit components. In order to achieve proper turn spacing, we coated copper wire with 25 μm of biocompatible polymer (Parylene C). Tuning and matching circuitry insured that the impedance of the RF coil was approximately 50 Ω at the operating frequency for 3-T proton MR applications. A duplexer was used to enable use of the microcoil catheter as a transceiver. Experimental verification of the coil design was achieved through ex vivo imaging of neural tissue. As expected, the microcoil catheter provided microscale images with 20-μm in-plane-resolution and 170-μm-thick slices. While 3-T MRI typically provides 1 to 30 voxels per-cubic-millimeter, in this paper we report that the MRI microcoil can provide hundreds, and even thousands of voxels in the same volume.

Reliability of glutamate and GABA quantification using proton magnetic resonance spectroscopy

The consistency and reliability of proton magnetic resonance spectroscopy (1H-MRS) assessments of neurotransmitter concentration has not been widely examined over multiple days. The purpose of this study was to determine the reliability of glutamate and GABA measures using a single-voxel 1H-MRS protocol in healthy men and women. Glutamate and GABA quantitations were obtained from the primary motor cortex (M1) and the dorsolateral prefrontal cortex (DLPFC) in 13 healthy individuals across 3 data collection sessions, including a baseline (Visit 1), 2-week (Visit 2), and 2-month time point (Visit 3). Glutamate concentrations were similar across visits in M1 (p=0.72) and the DLPFC (p=0.52). Reliability across days was excellent in M1 (R=0.93), and in the DLPFC (R=0.99). GABA concentrations were similar across visits in M1 (p=0.44) and in the DLPFC (p=0.59). Reliability of GABA concentration across days was excellent in M1 (R=0.93), and in the DLPFC (R=0.97). 1H-MRS is a reliable method for quantifying glutamate and GABA concentration in M1 and the DLPFC in humans.

An Implantable RF Solenoid for Magnetic Resonance Microscopy and Microspectroscopy

Miniature solenoids routinely enhance small volume nuclear magnetic resonance imaging and spectroscopy; however, no such techniques exist for patients. We present an implantable microcoil for diverse clinical applications, with a microliter coil volume. The design is loosely based on implantable depth electrodes, in which a flexible tube serves as the substrate, and a metal stylet is inserted into the tube during implantation. The goal is to provide enhanced signal-to-noise ratio (SNR) of structures that are not easily accessed by surface coils. The first-generation prototype was designed for implantation up to 2 cm, and provided initial proof-of-concept for microscopy. Subsequently, we optimized the design to minimize the influence of lead inductances, and to thereby double the length of the implantable depth (4 cm). The second-generation design represents an estimated SNR improvement of over 30% as compared to the original design when extended to 4 cm. Impedance measurements indicate that the device is stable for up to 24 h in body temperature saline. We evaluated the SNR and MR-related heating of the device at 3T. The implantable microcoil can differentiate fat and water peaks, and resolve submillimeter features.

Considerations For Small Detectors In High Reynolds Number Experiments

High Reynolds number experiments performed in liquid helium will require ultra-small detectors to measure spatial and temporal velocity profiles. In this paper we consider the many length and time scales involved and the limits to the scaling of detectors based on principles of hot-wire/film anemometry.

Nonequilibrium random telegraph switching in quantum point contacts

Abstract We have investigated nonequilibrium transport through quantum point contact structures in high mobility GaAs/AlGaAs heterostructure. For low source-drain bias the current-voltage characteristics show the expected conductance quantization. At biases above approximately 6 mV, conductance instabilities in the DC current-voltage characteristics are observed which depend on the thermal and light exposure history of the sample. Time-dependent measurements in the regions of instability reveal that random telegraph switching (RTS) between well-defined differential conductance states is occurring. The RTS has been studied as a function of source-drain and gate bias, as well as temperature. The average time in the low and high states is found to depend exponentially on the source-drain and gate bias around some critical bias point. This critical point appears to correspond to a transition when an extra quasi one-dimensional subband crosses the Fermi level. The origin of the switching is believed to be associated with the charging and discharging of shallow donor defects due to DX centers in the AlGaAs.

Validating DICOM Transcoding with an Open Multi-Format Resource

The Digital Imaging and Communications in Medicine (DICOM) standard has allowed wide-scale interoperability between medical imaging devices allowed for construction of large-scale radiological imaging system[1]. The DICOM standard provides for extensive structured meta-data ranging from the physical dimensions of the imaging data to patient military status. Moreover, “private” fields are permitted to store almost any additional data within DICOM datasets. These alternative fields are often used to store key acquisition parameters for new or emerging imaging sequence or assist interpretation of manufacturer specific settings. While DICOM provides for interoperability, there is ample room for interpretation or use of alternative coding strategies (e.g., storage of 3-D data in a light box array or as separate DICOM slices). Hence, interpreting DICOM data is a substantial process and can be manufacturer specific. The image processing research community has gravitated towards simpler but more explicit standardized research formats — first Analyze[2]and Minc[3], and more recently NIfTI[4]. Converting between data formats (known as transcoding) — either between files or between files and an internal memory representation — is a constant concern for software engineers and image processers (Figure 1). In medical imaging, it is critical that real-world orientation (e.g., right/left) and distances are preserved. Some image acquisitions have physical indications to allow orientation to be verified (e.g., using vitamin E capsules as fiducial markers in MRI), but these practices are inconsistent across sites. Software engineers have verified performance with the data that they have had available which can be limited in terms of manufactures and software release. Given typical research budgets, only data representative of current users is generally available and testing is difficult. Herein, we propose the “Rosetta bit” project to provide an open data resource to facilitate inter operability testing for image conversion in research software. Figure 1 DICOM can be converted into research file formats viewed with SPM[7], MIPAV[8]. 3D Slicer[9]. MRIcron[10], MATLAB (Mathworks, Natick, MA) The Rosetta bit provides a set of anonymized DICOM images along with validated conversion of the images into research file formats. The validation step consisted of using different visualization tools such as MIPAV, Slicer, SPM, etc… to check the orientation (e.g., left-right) of the converted data (Figure 1). This project specifically does not promote any particular converters, but rather encourages the data sponsor to use whatever methods they can validate for their data. Once the data have been correctly converted, others can test their preferred tools. We envision the Rosetta project as an evolving entity to which users can submit validated converted image sets and encourage software developers to support consistent image interpretation across data formats. A small logo can be used to designate that a software program has been tested with a specific release of the data resource. To test the converter, one developer can convert the raw data in the Rosetta bit project into his preferred converted format and validate it with the version present in the project. The contributors of the Rosetta bit project have provided a series of structural brain images. The initial database (Table 1) is a release of data from 4 different devices: GE SignaHD Excite, Siemens Trio, Philips Intera, and Philips 3T Achieva. All the data have been converted into NIfTI. The database provides 3D and 4D NIfTI. Many of the datasets were contributed to the public domain along with the MRIcron utilities; these data were converted with dcm2nii[5]. The Philips 3T Achieva dataset has been converted from DICOM to Philips PAR/REC and then from PAR/REC to NIFTI with r2agui (http://r2agui.sourceforge.net/). For all the data, the conversion from 4D NIFTI to 3D NIFTI used the SPM function spm_file_split. The data in the project has been manually anonymized using the software DicomBrowser[6] (http://nrg.wustl.edu/software/dicom-browser/). Table 1

Conductance instabilities in quantum point contacts

We present low-temperature electron transport measurements on quantum point contacts defined by electrostatic constrictions in the two-dimensional electron gas of a GaAs/AlGaAs heterostructure. Infrared illumination and annealing reversibly changes the nature of the electron transport through the point contact, from ideal point contact behavior to transport that shows two-level conductance fluctuations. In the ideal case, the dependence of the differential conductance on the bias across the contact is used to determine the shape of the transverse confining potential. In the non-ideal case, current-controlled negative differential conductance in the device characteristic is observed, and is shown to be the average of a two-level random telegraph signal. The random telegraph signal consists of fluctuations between two well-defined differential conductance states. We suggest the fluctuations are due to changes in the transverse confining potential caused by the dynamics of DX centers in the AlGaAs near the point contact.