[ { "key": "2RBD6E6W", "version": 1, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/2RBD6E6W", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/2RBD6E6W", "type": "text/html" } }, "meta": { "createdByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Smith et al.", "parsedDate": "2004", "numChildren": 0 }, "data": { "key": "2RBD6E6W", "version": 1, "itemType": "journalArticle", "title": "Advances in functional and structural MR image analysis and implementation as FSL", "creators": [ { "creatorType": "author", "firstName": "Stephen M.", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Mark", "lastName": "Jenkinson" }, { "creatorType": "author", "firstName": "Mark W.", "lastName": "Woolrich" }, { "creatorType": "author", "firstName": "Christian F.", "lastName": "Beckmann" }, { "creatorType": "author", "firstName": "Timothy E.J.", "lastName": "Behrens" }, { "creatorType": "author", "firstName": "Heidi", "lastName": "Johansen-Berg" }, { "creatorType": "author", "firstName": "Peter R.", "lastName": "Bannister" }, { "creatorType": "author", "firstName": "Marilena", "lastName": "De Luca" }, { "creatorType": "author", "firstName": "Ivana", "lastName": "Drobnjak" }, { "creatorType": "author", "firstName": "David E.", "lastName": "Flitney" }, { "creatorType": "author", "firstName": "Rami K.", "lastName": "Niazy" }, { "creatorType": "author", "firstName": "James", "lastName": "Saunders" }, { "creatorType": "author", "firstName": "John", "lastName": "Vickers" }, { "creatorType": "author", "firstName": "Yongyue", "lastName": "Zhang" }, { "creatorType": "author", "firstName": "Nicola", "lastName": "De Stefano" }, { "creatorType": "author", "firstName": "J. Michael", "lastName": "Brady" }, { "creatorType": "author", "firstName": "Paul M.", "lastName": "Matthews" } ], "abstractNote": "The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity, and scope of neuroimaging experiments. The development of such methodologies has allowed investigators to address scientific questions that could not previously be answered and, as such, has become an important research area in its own right.\nIn this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB). This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data. The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB's Software Library (FSL).", "publicationTitle": "NeuroImage", "publisher": "", "place": "", "date": "2004", "volume": "23", "issue": "Supplement 1", "section": "", "partNumber": "", "partTitle": "", "pages": "S208-S219", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.neuroimage.2004.07.051", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/B6WNP-4DD8GN8-3/2/6ac12c5eb9e31a1b5b3d32324c144489", "accessDate": "2010-01-09T23:03:15Z", "PMID": "", "PMCID": "", "ISSN": "1053-8119", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "FMRI", "type": 1 }, { "tag": "FSL", "type": 1 }, { "tag": "Structural MR image analysis", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2010-01-09T23:32:19Z", "dateModified": "2010-01-09T23:32:19Z" } }, { "key": "HVNDV3JV", "version": 1, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/HVNDV3JV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/HVNDV3JV", "type": "text/html" } }, "meta": { "createdByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Denk and Rauscher", "numChildren": 0 }, "data": { "key": "HVNDV3JV", "version": 1, "itemType": "journalArticle", "title": "Susceptibility Weighted Imaging With Multiple\nEchoes", "creators": [ { "creatorType": "author", "firstName": "Christian", "lastName": "Denk" }, { "creatorType": "author", "firstName": "Alexander", "lastName": "Rauscher" } ], "abstractNote": "", "publicationTitle": "Journal of Magnetic Resonance Imaging", "publisher": "", "place": "", "date": "", "volume": "in press", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-11-21T01:55:48Z", "dateModified": "2009-11-21T01:55:48Z" } }, { "key": "TIPJXP4I", "version": 2, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/TIPJXP4I", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/TIPJXP4I", "type": "text/html" } }, "meta": { "createdByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Portnoy and Stanisz", "parsedDate": "2007-07", "numChildren": 0 }, "data": { "key": "TIPJXP4I", "version": 2, "itemType": "journalArticle", "title": "Modeling pulsed magnetization transfer", "creators": [ { "creatorType": "author", "firstName": "Sharon", "lastName": "Portnoy" }, { "creatorType": "author", "firstName": "Greg J", "lastName": "Stanisz" } ], "abstractNote": "Modeling the effects of clinical magnetization transfer (MT) scans, which generate contrast using short, shaped radiofrequency (RF) pulses (pulsed MT), is complex and time-consuming. As a result, several studies have proposed approximate methods for a simplified analysis of the experimental data. However, potential differences in the MT parameters estimated by each method may complicate the comparison of reported results. In this study we evaluated three approximate methods currently used in quantitative MT (qMT) studies. In the first part of the investigation, an MT modeling technique that makes minimal approximations, other than the use of a two-pool tissue representation, was developed and validated. Subsequently, this technique served as a standard against which to evaluate the other, more approximate models. Each model was used to fit experimental data from samples of wild-type (WT) and shiverer mouse spinal cord, as well as simulated data generated by our minimal approximation modeling technique. The results of this study demonstrate that the approximations used in pulsed MT modeling are quite robust. In particular, it was shown that the semisolid pool fraction, M(0)(B), which is known to correlate strongly with myelin content, and the transverse relaxation time of macromolecular protons, T(2)(B), could be evaluated with reasonable accuracy regardless of the model used.", "publicationTitle": "Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine", "publisher": "", "place": "", "date": "Jul 2007", "volume": "58", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "144-155", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Magn Reson Med", "DOI": "10.1002/mrm.21244", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/17659607", "accessDate": "2009-10-16T20:36:47Z", "PMID": "17659607", "PMCID": "", "ISSN": "0740-3194", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Brain Diseases", "type": 1 }, { "tag": "Magnetic Resonance Imaging", "type": 1 }, { "tag": "Mice", "type": 1 }, { "tag": "Models, Theoretical", "type": 1 }, { "tag": "Spinal Cord", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-10-16T20:37:25Z", "dateModified": "2009-10-16T20:37:25Z" } }, { "key": "Z7TIXW8Z", "version": 2, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/Z7TIXW8Z", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/Z7TIXW8Z", "type": "text/html" } }, "meta": { "createdByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Sedlacik et al.", "parsedDate": "2007-11", "numChildren": 1 }, "data": { "key": "Z7TIXW8Z", "version": 2, "itemType": "journalArticle", "title": "Obtaining blood oxygenation levels from MR signal behavior in the presence of single venous vessels", "creators": [ { "creatorType": "author", "firstName": "Jan", "lastName": "Sedlacik" }, { "creatorType": "author", "firstName": "Alexander", "lastName": "Rauscher" }, { "creatorType": "author", "firstName": "Jürgen R", "lastName": "Reichenbach" } ], "abstractNote": "The MR signal decay in gradient echo sequences includes signal loss due to spin dephasing caused by static magnetic field inhomogeneities. This decay can be calculated for different geometries of the susceptibility distribution, such as spheres, cylinders, or cylinder networks. In particular, the model of an infinitely long cylinder is a good approximation for single straight blood vessels. Blood oxygenation and blood volume fraction are important parameters, which influence the signal in a characteristic way. In this work the signal decays for a single cylindrical vessel were investigated and evaluated in simulations, phantom measurements as well as in vivo measurements of small single veins in the human brain by using a 3D multiecho gradient echo sequence. Good agreement between simulations and phantom experiments was obtained for different experimental settings. Based on the simulations, physiologically consistent values of venous blood oxygenation level, Y, were extracted from the in vivo measurements of different veins and volunteers (Y = 0.55 +/- 0.02). The methods ability to measure changes in venous blood oxygenation induced by carbogen breathing was demonstrated in one volunteer, where an increase from Y approximately 0.5 to Y approximately 0.7 was observed.", "publicationTitle": "Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine", "publisher": "", "place": "", "date": "Nov 2007", "volume": "58", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "1035-44", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Magn Reson Med", "DOI": "10.1002/mrm.21283", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/17969121", "accessDate": "2008-11-28T17:51:12Z", "PMID": "17969121", "PMCID": "", "ISSN": "0740-3194", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Magnetic Resonance Imaging", "type": 1 }, { "tag": "Oxygen", "type": 1 }, { "tag": "Phantoms, Imaging", "type": 1 }, { "tag": "Veins", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-10-14T00:49:46Z", "dateModified": "2009-10-14T00:49:46Z" } }, { "key": "K4XBXPBU", "version": 1, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/K4XBXPBU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/K4XBXPBU", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/4875/items/Z7TIXW8Z", "type": "application/json" } }, "meta": { "createdByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } } }, "data": { "key": "K4XBXPBU", "version": 1, "parentItem": "Z7TIXW8Z", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Snapshot", "accessDate": "2008-11-28T17:51:25Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/17969121?dopt=AbstractPlus", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2009-10-14T00:49:46Z", "dateModified": "2009-10-14T00:49:46Z" } }, { "key": "5TPTW67S", "version": 2, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/5TPTW67S", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/5TPTW67S", "type": "text/html" } }, "meta": { "createdByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Deistung et al.", "parsedDate": "2008-11", "numChildren": 1 }, "data": { "key": "5TPTW67S", "version": 2, "itemType": "journalArticle", "title": "Susceptibility weighted imaging at ultra high magnetic field strengths: theoretical considerations and experimental results", "creators": [ { "creatorType": "author", "firstName": "Andreas", "lastName": "Deistung" }, { "creatorType": "author", "firstName": "Alexander", "lastName": "Rauscher" }, { "creatorType": "author", "firstName": "Jan", "lastName": "Sedlacik" }, { "creatorType": "author", "firstName": "Jörg", "lastName": "Stadler" }, { "creatorType": "author", "firstName": "Stephan", "lastName": "Witoszynskyj" }, { "creatorType": "author", "firstName": "Jürgen R", "lastName": "Reichenbach" } ], "abstractNote": "We present numerical simulations and experimental results for susceptibility weighted imaging (SWI) at 7 T. Magnitude, phase, and SWI contrast were simulated for different voxel geometries and imaging parameters, resulting in an echo time of 14 msec for optimum contrast between veins and surrounding tissue. Slice thickness of twice the in-plane voxel size or more resulted in optimum vessel visibility. Phantom and in vivo data are in very good agreement with the simulations and the delineation of vessels at 7 T was superior compared to lower field strengths. The phase of the complex data reveals anatomical details that are complementary to the corresponding magnitude images. Susceptibility weighted imaging at very high field strengths is a promising technique because of its high sensitivity to tissue susceptibility, its low specific absorption rate, and the phase's negligible sensitivity to B(1) inhomogeneities.", "publicationTitle": "Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine", "publisher": "", "place": "", "date": "Nov 2008", "volume": "60", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "1155-68", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Magn Reson Med", "DOI": "10.1002/mrm.21754", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18956467", "accessDate": "2008-11-28T17:51:11Z", "PMID": "18956467", "PMCID": "", "ISSN": "1522-2594", "archive": "", "archiveLocation": "", "shortTitle": "Susceptibility weighted imaging at ultra high magnetic field strengths", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-10-14T00:49:25Z", "dateModified": "2009-10-14T00:49:25Z" } }, { "key": "7F4ZEJE6", "version": 1, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/7F4ZEJE6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/7F4ZEJE6", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/4875/items/5TPTW67S", "type": "application/json" } }, "meta": { "createdByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } } }, "data": { "key": "7F4ZEJE6", "version": 1, "parentItem": "5TPTW67S", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Snapshot", "accessDate": "2008-11-28T17:51:32Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18956467?dopt=AbstractPlus", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2009-10-14T00:49:25Z", "dateModified": "2009-10-14T00:49:25Z" } }, { "key": "F364ZE99", "version": 2, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/F364ZE99", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/F364ZE99", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25060, "username": "elcris", "name": "Christian Denk", "links": { "alternate": { "href": "https://www.zotero.org/elcris", "type": "text/html" } } }, "lastModifiedByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Péran et al.", "parsedDate": "2007-12", "numChildren": 0 }, "data": { "key": "F364ZE99", "version": 2, "itemType": "journalArticle", "title": "Voxel-based analysis of R2* maps in the healthy human brain", "creators": [ { "creatorType": "author", "firstName": "Patrice", "lastName": "Péran" }, { "creatorType": "author", "firstName": "Gisela", "lastName": "Hagberg" }, { "creatorType": "author", "firstName": "Giacomo", "lastName": "Luccichenti" }, { "creatorType": "author", "firstName": "Andrea", "lastName": "Cherubini" }, { "creatorType": "author", "firstName": "Valentina", "lastName": "Brainovich" }, { "creatorType": "author", "firstName": "Pierre", "lastName": "Celsis" }, { "creatorType": "author", "firstName": "Carlo", "lastName": "Caltagirone" }, { "creatorType": "author", "firstName": "Umberto", "lastName": "Sabatini" } ], "abstractNote": "PURPOSE: To develop a voxel-based analysis of an R2* map of healthy human brain that is automatic, reproducible, and realizable in a single examination on a 3T MR imager. Such a tool could be useful to measure iron accumulation in neurodegenerative diseases. MATERIALS AND METHODS: In all, 18 healthy subjects underwent MR imaging at a field strength of 3T: 1) six consecutive T2*-weighted gradient-echo volumes were acquired using a segmented echo-planar imaging sequence and 2) a conventional dual-echo turbo spin echo sequence was also applied to acquire T2-weighted images. Images were realigned and spatial correction was performed using a template brain dataset with SPM2. For each subject we performed a voxel-by-voxel nonlinear least-squares fitting of the data acquired at the six echo times to obtain a monoexponential signal decay curve. The reproducibility and sensitivity to age variation were assessed by voxel-based analysis. RESULTS: The reproducibility tests in whole brain analysis showed little R2* variation. Furthermore, the statistical analysis, performed on each brain voxel, revealed a significant positive correlation between age and MR values located in regions where a slow and constant age-related iron deposition is known. CONCLUSION: Our method, combining data acquisition and data processing, demonstrates the feasibility of voxel-based analysis on an R2* map and affords a high degree of sensitivity and good reproducibility while maintaining high spatial resolution.", "publicationTitle": "Journal of Magnetic Resonance Imaging: JMRI", "publisher": "", "place": "", "date": "Dec 2007", "volume": "26", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "1413-1420", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Magn Reson Imaging", "DOI": "10.1002/jmri.21204", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18059009", "accessDate": "2009-10-09T00:21:43Z", "PMID": "18059009", "PMCID": "", "ISSN": "1053-1807", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Adult", "type": 1 }, { "tag": "Artifacts", "type": 1 }, { "tag": "Brain Mapping", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Image Enhancement", "type": 1 }, { "tag": "Image Processing, Computer-Assisted", "type": 1 }, { "tag": "Least-Squares Analysis", "type": 1 }, { "tag": "Magnetic Resonance Imaging", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "Reproducibility of Results", "type": 1 }, { "tag": "Sensitivity and Specificity", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-10-09T00:24:40Z", "dateModified": "2009-10-09T00:24:40Z" } }, { "key": "VVPXDT4G", "version": 2, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/VVPXDT4G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/VVPXDT4G", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25060, "username": "elcris", "name": "Christian Denk", "links": { "alternate": { "href": "https://www.zotero.org/elcris", "type": "text/html" } } }, "lastModifiedByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Du et al.", "parsedDate": "2009-08", "numChildren": 0 }, "data": { "key": "VVPXDT4G", "version": 2, "itemType": "journalArticle", "title": "Multi-echo acquisition of MR angiography and venography of the brain at 3 Tesla", "creators": [ { "creatorType": "author", "firstName": "Yiping P", "lastName": "Du" }, { "creatorType": "author", "firstName": "Zhaoyang", "lastName": "Jin" }, { "creatorType": "author", "firstName": "Yuzheng", "lastName": "Hu" }, { "creatorType": "author", "firstName": "Jody", "lastName": "Tanabe" } ], "abstractNote": "PURPOSE: To improve the visibility of veins in susceptibility-weighted imaging (SWI) using a multi-gradient echo acquisition. MATERIALS AND METHODS: A three-dimensional multi-echo gradient-echo pulse sequence was developed for simultaneous acquisition of MR angiography and multiple volumes of MR venography (MRV) of the brain. The first echo was acquired for MR angiography using the time-of-flight in-flow effect. The subsequent echoes were acquired for SWI-based MRV at different echo times (TEs). RESULTS: Multiple MRV datasets acquired at different TEs were complementary in depicting the venous vasculature. MRV data acquired at a longer TE had a higher venous contrast and stronger susceptibility weighting, whereas MRV data acquired at a shorter TE had a higher signal-to-noise ratio and less severe off-resonance artifacts. Three-dimensional mapping of local field gradients was calculated and the transverse relaxivity (R(2)) at each voxel was quantified using multi-TE exponential fitting. CONCLUSION: Multi-echo acquisition of MR angiography and venography demonstrated improved visibility of venous vasculature especially in regions with severe field inhomogeneity compared with conventional acquisition of SWI and dual-echo acquisition of MR angiography and venography.", "publicationTitle": "Journal of Magnetic Resonance Imaging: JMRI", "publisher": "", "place": "", "date": "Aug 2009", "volume": "30", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "449-454", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Magn Reson Imaging", "DOI": "10.1002/jmri.21833", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19629975", "accessDate": "2009-08-14T19:31:18Z", "PMID": "19629975", "PMCID": "", "ISSN": "1053-1807", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-10-09T00:24:31Z", "dateModified": "2009-10-09T00:24:31Z" } }, { "key": "I2GSUZGT", "version": 2, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/I2GSUZGT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/I2GSUZGT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25060, "username": "elcris", "name": "Christian Denk", "links": { "alternate": { "href": "https://www.zotero.org/elcris", "type": "text/html" } } }, "lastModifiedByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Krüger and Glover", "parsedDate": "2001-10", "numChildren": 0 }, "data": { "key": "I2GSUZGT", "version": 2, "itemType": "journalArticle", "title": "Physiological noise in oxygenation-sensitive magnetic resonance imaging", "creators": [ { "creatorType": "author", "firstName": "G", "lastName": "Krüger" }, { "creatorType": "author", "firstName": "G H", "lastName": "Glover" } ], "abstractNote": "The physiological noise in the resting brain, which arises from fluctuations in metabolic-linked brain physiology and subtle brain pulsations, was investigated in six healthy volunteers using oxygenation-sensitive dual-echo spiral MRI at 3.0 T. In contrast to the system and thermal noise, the physiological noise demonstrates a signal strength dependency and, unique to the metabolic-linked noise, an echo-time dependency. Variations of the MR signal strength by changing the flip angle and echo time allowed separation of the different noise components and revealed that the physiological noise at 3.0 T (1) exceeds other noise sources and (2) is significantly greater in cortical gray matter than in white matter regions. The SNR in oxygenation-sensitive MRI is predicted to saturate at higher fields, suggesting that noise measurements of the resting brain at 3.0 T and higher may provide a sensitive probe of functional information.", "publicationTitle": "Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine", "publisher": "", "place": "", "date": "Oct 2001", "volume": "46", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "631-637", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Magn Reson Med", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/11590638", "accessDate": "2009-10-09T00:23:59Z", "PMID": "11590638", "PMCID": "", "ISSN": "0740-3194", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Adult", "type": 1 }, { "tag": "Artifacts", "type": 1 }, { "tag": "Brain", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Magnetic Resonance Imaging", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-10-09T00:24:11Z", "dateModified": "2009-10-09T00:24:11Z" } }, { "key": "94NIJ5W5", "version": 2, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/94NIJ5W5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/94NIJ5W5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25060, "username": "elcris", "name": "Christian Denk", "links": { "alternate": { "href": "https://www.zotero.org/elcris", "type": "text/html" } } }, "lastModifiedByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Haacke et al.", "parsedDate": "2004-09", "numChildren": 0 }, "data": { "key": "94NIJ5W5", "version": 2, "itemType": "journalArticle", "title": "Susceptibility weighted imaging (SWI)", "creators": [ { "creatorType": "author", "firstName": "E M", "lastName": "Haacke" }, { "creatorType": "author", "firstName": "Yingbiao", "lastName": "Xu" }, { "creatorType": "author", "firstName": "Yu-Chung N", "lastName": "Cheng" }, { "creatorType": "author", "firstName": "Jürgen R", "lastName": "Reichenbach" } ], "abstractNote": "Susceptibility differences between tissues can be utilized as a new type of contrast in MRI that is different from spin density, T1-, or T2-weighted imaging. Signals from substances with different magnetic susceptibilities compared to their neighboring tissue will become out of phase with these tissues at sufficiently long echo times (TEs). Thus, phase imaging offers a means of enhancing contrast in MRI. Specifically, the phase images themselves can provide excellent contrast between gray matter (GM) and white matter (WM), iron-laden tissues, venous blood vessels, and other tissues with susceptibilities that are different from the background tissue. Also, for the first time, projection phase images are shown to demonstrate tissue (vessel) continuity. In this work, the best approach for combining magnitude and phase images is discussed. The phase images are high-pass-filtered and then transformed to a special phase mask that varies in amplitude between zero and unity. This mask is multiplied a few times into the original magnitude image to create enhanced contrast between tissues with different susceptibilities. For this reason, this method is referred to as susceptibility-weighted imaging (SWI). Mathematical arguments are presented to determine the number of phase mask multiplications that should take place. Examples are given for enhancing GM/WM contrast and water/fat contrast, identifying brain iron, and visualizing veins in the brain.", "publicationTitle": "Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine", "publisher": "", "place": "", "date": "Sep 2004", "volume": "52", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "612-8", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Magn Reson Med", "DOI": "10.1002/mrm.20198", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/15334582", "accessDate": "2009-03-30T18:16:24Z", "PMID": "15334582", "PMCID": "", "ISSN": "0740-3194", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Body Water", "type": 1 }, { "tag": "Brain", "type": 1 }, { "tag": "Cerebrovascular Circulation", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Iron", "type": 1 }, { "tag": "Lipid Metabolism", "type": 1 }, { "tag": "Magnetic Resonance Imaging", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-09-16T03:20:14Z", "dateModified": "2009-09-25T21:42:42Z" } }, { "key": "VZNNBSSK", "version": 2, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/VZNNBSSK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/VZNNBSSK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25060, "username": "elcris", "name": "Christian Denk", "links": { "alternate": { "href": "https://www.zotero.org/elcris", "type": "text/html" } } }, "lastModifiedByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Vaillancourt et al.", "parsedDate": "2009-04-21", "numChildren": 0 }, "data": { "key": "VZNNBSSK", "version": 2, "itemType": "journalArticle", "title": "High-resolution diffusion tensor imaging in the substantia nigra of de novo Parkinson disease", "creators": [ { "creatorType": "author", "firstName": "D E", "lastName": "Vaillancourt" }, { "creatorType": "author", "firstName": "M B", "lastName": "Spraker" }, { "creatorType": "author", "firstName": "J", "lastName": "Prodoehl" }, { "creatorType": "author", "firstName": "I", "lastName": "Abraham" }, { "creatorType": "author", "firstName": "D M", "lastName": "Corcos" }, { "creatorType": "author", "firstName": "X J", "lastName": "Zhou" }, { "creatorType": "author", "firstName": "C L", "lastName": "Comella" }, { "creatorType": "author", "firstName": "D M", "lastName": "Little" } ], "abstractNote": "BACKGROUND: In the midbrain of patients with Parkinson disease (PD), there is a selective loss of dopaminergic neurons in the ventrolateral and caudal substantia nigra (SN). In a mouse model of PD, investigators have administered 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and found that measures derived using diffusion tensor imaging (DTI) were correlated with the number of dopamine neurons lost following intoxication. METHODS: Twenty-eight subjects (14 with early stage, untreated PD and 14 age- and gender-matched controls) were studied with a high-resolution DTI protocol at 3 Tesla using an eight-channel phase array coil and parallel imaging to study specific segments of degeneration in the SN. Regions of interest were drawn in the rostral, middle, and caudal SN by two blinded and independent raters. RESULTS: Fractional anisotropy (FA) was reduced in the SN of subjects with PD compared with controls (p < 0.001). Post hoc analysis identified that reduced FA for patients with PD was greater in the caudal compared with the rostral region of interest (p < 0.00001). A receiver operator characteristic analysis in the caudal SN revealed that sensitivity and specificity were 100% for distinguishing patients with PD from healthy subjects. Findings were consistent across both raters. CONCLUSIONS: These findings provide evidence that high resolution diffusion tensor imaging in the substantia nigra distinguishes early stage, de novo patients with Parkinson disease (PD) from healthy individuals on a patient by patient basis and has the potential to serve as a noninvasive early biomarker for PD.", "publicationTitle": "Neurology", "publisher": "", "place": "", "date": "Apr 21, 2009", "volume": "72", "issue": "16", "section": "", "partNumber": "", "partTitle": "", "pages": "1378-1384", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Neurology", "DOI": "10.1212/01.wnl.0000340982.01727.6e", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19129507", "accessDate": "2009-09-25T17:18:23Z", "PMID": "19129507", "PMCID": "", "ISSN": "1526-632X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Adult", "type": 1 }, { "tag": "Aged", "type": 1 }, { "tag": "Anisotropy", "type": 1 }, { "tag": "Biological Markers", "type": 1 }, { "tag": "Diagnosis, Differential", "type": 1 }, { "tag": "Diffusion", "type": 1 }, { "tag": "Diffusion Magnetic Resonance Imaging", "type": 1 }, { "tag": "Disease Progression", "type": 1 }, { "tag": "Dopamine", "type": 1 }, { "tag": "Early Diagnosis", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "Middle Aged", "type": 1 }, { "tag": "Nerve Degeneration", "type": 1 }, { "tag": "Neurons", "type": 1 }, { "tag": "Parkinson Disease", "type": 1 }, { "tag": "Predictive Value of Tests", "type": 1 }, { "tag": "Reproducibility of Results", "type": 1 }, { "tag": "Severity of Illness Index", "type": 1 }, { "tag": "Substantia Nigra", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-09-25T17:18:25Z", "dateModified": "2009-09-25T17:18:25Z" } }, { "key": "HNT485ME", "version": 2, "library": { "type": "group", "id": 4875, "name": "Reproduc_Paper", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4875/items/HNT485ME", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproduc_paper/items/HNT485ME", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25060, "username": "elcris", "name": "Christian Denk", "links": { "alternate": { "href": "https://www.zotero.org/elcris", "type": "text/html" } } }, "lastModifiedByUser": { "id": 11623, "username": "schneegestoeber", "name": "Alexander Rauscher", "links": { "alternate": { "href": "https://www.zotero.org/schneegestoeber", "type": "text/html" } } }, "creatorSummary": "Martin et al.", "parsedDate": "2008-04-15", "numChildren": 0 }, "data": { "key": "HNT485ME", "version": 2, "itemType": "journalArticle", "title": "Midbrain iron content in early Parkinson disease: a potential biomarker of disease status", "creators": [ { "creatorType": "author", "firstName": "W R Wayne", "lastName": "Martin" }, { "creatorType": "author", "firstName": "Marguerite", "lastName": "Wieler" }, { "creatorType": "author", "firstName": "Myrlene", "lastName": "Gee" } ], "abstractNote": "BACKGROUND: Parkinson disease (PD) is a progressive neurodegenerative disorder in which the major pathologic substrate is a loss of dopaminergic neurons from the lateral substantia nigra pars compacta (SNc). Our objective was to determine whether, in patients with early PD, SNc changes evident on MRI sequences sensitive to iron content corresponded anatomically to the pathologic changes reported previously, and to correlate these changes to the duration and severity of clinical manifestations of PD. METHODS: Twenty-six untreated patients with early PD and 13 age- and gender-matched control subjects had MRI with a 3 tesla magnet using a multiple gradient echo sequence designed for rapid single-scan mapping of the proton transverse relaxation rate (R(2)*). R(2)* was calculated for midbrain and forebrain basal ganglia regions. Clinical features were rated with the Unified Parkinson's Disease Rating Scale. RESULTS: A difference in measured R(2)* values between patients and controls was observed in the lateral SNc (p