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Data acquired during the development of an R2′ mapping technique with prospective correction for macroscopic magnetic field gradients
No full textThe data in this archive was acquired during the development of the GASE (Gradient-Echo Slice Excitation Imaging Asymmetric Spin Echo; GESEPI ASE) technique. GASE can be used to map the reversible transverse relaxation rate R2′ (a contrast used in Magnetic Resonance Imaging - MRI) without the need to separately acquire a magnetic field map to correct for residual magnetic field gradients not compensated by magnet shimming. This technique has application in measuring blood oxygenation using the quantitative BOLD (1,2) (baseline levels) and calibrated BOLD (3) (dynamic changes) techniques as well as iron deposition (4).
This dataset consists of three experiments;
- phantom.zip containing an initial validation of the GASE technique.
- fmapping.zip used to investigate the distribution of magnetic field gradients in the head.
- gesepi.zip where a range of GASE variants were tested against uncorrected ASE.
Images are encoded as compressed NIFTI files and contain basic information about voxel size, repetition time and orientation. Further information is contained in a YAML formatted file, which is both human and machine readable. These files are inherited by image files at lower levels of the directory structure unless they are overridden by a file at the lower level.
Phantom data - phantom.zip
This dataset consists of ASE and GASE4 images acquired with different applied magnetic field gradients in the z-direction: 0, 100, 150 microTesla/meter. A standard phantom based on the FBIRN agar doped construction was used.
Field mapping data - fmapping.zip
This dataset consists of high resolution magnetic field maps in order to investigate the distribution of magnetic field gradients in healthy volunteers. High resolution Magnetisation Prepared RApid Gradient Echo (MPRAGE) images for each subject were acquired for coregistration and segmentation purposes. MPRAGE images are brain extracted (5) in order to preserve anonymity of the subjects.
GESEPI data - gesepi.zip
This dataset consists of 4 different ASE variants for comparison with standard ASE: GASE4, GASE8 and GASE128 (see glossary below). High resolution MPRAGE images for each subject were acquired for coregistration and segmentation purposes. MPRAGE images are brain extracted (5) in order to preserve anonymity of the subjects.
See each individual directory for file naming conventions.
Glossary
EPI - Echo Planar Imaging
ASE - Standard Asymmetric Spin Echo data acquired with EPI
GASE4 - GESEPI ASE data acquired with 4 subslices (partitions) at 1.24mm each with 3D EPI
GASE8 - GESEPI ASE data acquired with 8 subslices (partitions) at 0.63mm each with 3D EPI
GASE128 - GASE4 data with doubled in-plane resolution from 64 to 128 matrix
References
1. An H, Lin W. Quantitative measurements of cerebral blood oxygen saturation using magnetic resonance imaging. J. Cereb. Blood Flow Metab. 2000;20:1225–1236. doi: 10.1097/00004647-200008000-00008.
2. He X, Yablonskiy DA. Quantitative BOLD: Mapping of human cerebral deoxygenated blood volume and oxygen extraction fraction: Default state. Magn. Reson. Med. 2007;57:115–126. doi: 10.1002/mrm.21108.
3. Blockley NP, Griffeth VEM, Simon AB, Dubowitz DJ, Buxton RB. Calibrating the BOLD response without administering gases: Comparison of hypercapnia calibration with calibration using an asymmetric spin echo. Neuroimage 2015;104:423–429. doi: 10.1016/j.neuroimage.2014.09.061.
4. Ordidge RJ, Gorell JM, Deniau JC, Knight RA, Helpern JA. Assessment of relative brain iron concentrations using T2-weighted and T2*-weighted MRI at 3 Tesla. Magn. Reson. Med. 1994;32:335–341.
5. Smith SM. Fast robust automated brain extraction. Hum. Brain Mapp. 2002;17:143–155. doi: 10.1002/hbm.10062
Data acquired to demonstrate a streamlined approach to mapping and quantifying brain oxygenation using quantitative BOLD
No full textThis dataset will form the basis of a forthcoming publication regarding streamlining of the quantitative BOLD (qBOLD) approach to measuring brain oxygenation. In the absence of a reference to this publication the methods used are outlined here. Please reference this dataset if you use it in your work.
Stone AJ, Blockley NP. Data acquired to demonstrate a streamlined approach to mapping and quantifying brain oxygenation using quantitative BOLD. Oxford University Research Archive 2016. doi:
*Summary*
This dataset was acquired during the development of a streamlined qBOLD technique for making measurements of brain oxygenation. The aim here was to see whether confounding partial volume effects of multiple tissue types could be removed using an inversion recovery preparation. Inversion times were optimised to null cerebrospinal fluid (CSF), grey matter (GM) or white matter (WM) at the time of image acquisition [1]. Images were acquired using an Asymmetric Spin Echo (ASE) pulse sequence to introduce varying amount of R2′ weighting to images [2]. R2′ (R-2-prime) is the reversible relaxation rate, a component of transverse signal decay and the reciprocal of T2′ (T-2-prime). Gradient Echo Slice Excitation Profile Imaging (GESEPI) was incorporated into the ASE acquisition to minimise the effect of through-slice magnetic field gradients which would otherwise artificially elevate R2′ [3].
*MRI data*
Images were acquired using a Siemens Magnetom Verio scanner at 3T. The body coil was used for transmission and the manufacturer's 32-channel head coil was used for reception. GESEPI ASE (GASE) data were acquired with a field of view of 240x240 mm2, a 64x64 matrix, ten 5mm slices, TR/TE=3s/74ms and an EPI bandwidth of 2004Hx/px. ASE images are acquired with varying amount of R2′ weighting determined by the spin echo displacement time, tau, i.e. S = S0 exp(-tau R2′) exp(-TE R2). Twenty four values of tau were acquired for each GASE scan: -28, -24, -20, -16, -12, -8, -4, 0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60 and 64ms. The GESEPI magnetic field gradient correction technique required each 5mm slice to be encoded into multiple thin partitions each 1.25mm thick. Furthermore, partitions were oversampled by 100% leading to the acquisition of 8 partitions per slice. Oversampled slices were discarded during reconstruction, resulting in 40 slices being acquired for each tau value. To regain signal to noise ratio we suggest summing the slices in blocks of four, therefore resulting in the original ten prescribed slices. A slice selective inversion recovery preparation was used to null the signal of a target tissue compartment. The appropriate inversion time for each compartment was optimised based on literature values for CSF, GM and WM [4], to give values of 1.21s, 0.702s and 0.511s, respectively. In addition, one dataset was acquired without an inversion recovery preparation with the same range of tau values and one dataset was acquired with an expanded foot-head coverage for only tau=0ms - the spin echo - to help with registration. High resolution T1 weighted anatomical images were also acquired for registration and the generation of tissue specific masks. Anatomicals are "defaced" using the shell script in the code directory [5].
*Data curation*
The structure in which this data has been placed is based on the Brain Imaging Data Structure (BIDS) format [6]. However, this format (BIDS version 1.0.0-rc2) does not support ASE data, but we have followed the guiding principles of this specification.
*References*
1. Hajnal JV, Bryant DJ, Kasuboski L, Pattany PM, De Coene B, Lewis PD, Pennock JM, Oatridge A, Young IR, Bydder GM. Use of fluid attenuated inversion recovery (FLAIR) pulse sequences in MRI of the brain. J Comput Assist Tomogr 1992;16:841–844.
2. Wismer GL, Buxton RB, Rosen BR, Fisel CR, Oot RF, Brady TJ, Davis KR. Susceptibility induced MR line broadening: applications to brain iron mapping. J Comput Assist Tomogr 1988;12:259–265.
3. Blockley NP, Stone AJ. Improving the specificity of R2′ to the deoxyhaemoglobin content of brain tissue: Prospective correction of macroscopic magnetic field gradients. Neuroimage 2016, in press. doi: 10.1016/j.neuroimage.2016.04.013
4. Shen Y, Kauppinen RA, Vidyasagar R, Golay X. A functional magnetic resonance imaging technique based on nulling extravascular gray matter signal. Journal of Cerebral Blood Flow & Metabolism 2008;29:144–156. doi: 10.1038/jcbfm.2008.96.
5. https://github.com/hanke/gumpdata/blob/master/scripts/conversion/convert_dicoms_anatomy
6. http://bids.neuroimaging.i
Data generated by a Monte Carlo based simple vessel simulation of the ASE qBOLD signal
No full textThe data in this archive was generated using a Monte Carlo based numerical simulation of the extravascular blood oxygenation level dependent effect (BOLD) MRI signal. This data will underpin a forthcoming publication investigating systematic error in the asymmetric spin echo (ASE) quantitative BOLD (qBOLD) technique. Please reference this dataset if you use it in your work. Stone AJ, Holland NC, Berman AJL, Blockley NP. Data generated by a Monte Carlo based simple vessel simulation of the ASE qBOLD signal. Oxford University Research Archive 2019. See ORA record for DOI.
The archive consists of multiple data sets, which are saved as MATLAB .mat files. Each folder contains one .mat file for each simulated vessel radius with the format simvessim_resX.mat, where X is the vessel radius in micrometers. Basic physiological parameters are varied for each folder, which can be found in the MATLAB structure p contained within each .mat file
Data acquired to investigate new approaches to cerebrovascular reactivity mapping using MRI
No full textThe data in this archive was acquired to investigate several new approaches to cerebrovascular reactivity mapping using MRI and will form the basis of forthcoming publications. Please reference this dataset if you use it in your work.
Blockley NP, Harkin JW, Stone AJ, Bulte DP. Data acquired to investigate new approaches to cerebrovascular reactivity mapping using MRI. Oxford University Research Archive 2017. doi: 10.5287/bodleian:Xk48adQAO
Data sets consist of (in order of acquisition):
1. Single post-labelling delay PCASL during a hypercapnia block paradigm
2. Multiple post-labelling delay PCASL at steady state normocapnia
3. Multiple post-labelling delay PCASL at steady state hypercapnia
4. Single TE BOLD-weighted imaging with Toronto hypercapnia block protocol
5. Single TE BOLD-weighted imaging with Sinusoidal hypercapnia protocol
6. Multiple Tau value R2'-weighted imaging with GASE acquisition
7. High resolution T1-weighted anatomical imaging
8. Respiratory data including end-tidal O2 and CO2
9. Pre-scan resting physiological data
Images are encoded as compressed NIFTI files and contain basic information about voxel size, repetition time and orientation. Further information is contained in a JSON file, which is both human and machine readable. These files are inherited by image files at lower levels of the directory structure unless they are overridden by a file at the lower level. In this way the data structure follows the Brain Imaging Data Structure (BIDS) version 1.0.0-rc2.
See README for further details
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Chemical exchange saturation transfer methods for clinical magnetic resonance imaging
No full textChemical exchange saturation transfer (CEST) imaging is a novel contrast mechanism in magnetic resonance imaging. CEST allows for the indirect detection of chemical groups that contain exchangeable protons. The contrast from endogenous CEST agents in the human brain is sensitive to changes in pH and protein structures. Therefore, CEST imaging offers a potential tool for the non-invasive detection of pathologies such as stroke and cancer.
However, clinical implementation of current CEST MRI sequences is hindered by a lack of contrast-to-noise ratio (CNR) per unit time. Furthermore, confounding effects which contribute to the development of CEST contrast make interpretation of this contrast difficult. This thesis examines the underlying physical effects that govern the development of CEST contrast and aims to improve clinical CEST sequences.
The ability to correctly identify CEST parameters from z-spectra was investigated through simulations of the Bloch-McConnell equations. Conventional least squares fitting methods are inherently sensitive to changes in the bulk water. Reducing the sampling of the bulk water frequencies improved the sensitivity of this method to the exchange rate.
In vitro experiments using conventional non-interleaved CEST sequences demonstrated that reduction of the longitudinal magnetisation close to the bulk water frequencies is dominated by T1 relaxation. Minimisation of the inversions of the bulk water reduced the longitudinal component of the direct water saturation (DWS) effect. Implementation of additional acquisition events allowed for the transverse component of DWS to be used for imaging.
Interleaved CEST sequences were used in phantoms to study the effect of the interleaved readout excitations. Optimal flip angles, ð¼, for the readout pulses fulfilled the  condition 0 < α < αernst and allowed compromise between optimal CEST contrast and signal-to-noise ratio (SNR). Reducing SNR in favour of CNR made the interleaved CEST sequences more prone to coherence pathway artefacts. Hexagonal spoiling in interleaved CEST reduced this problem.
Finally, in vivo experiments showed that confounding effects such as T1 can be used as a contrast mechanism to optimise CEST sequences directly in healthy volunteers where conventional stroke contrasts are lacking.</p
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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