Main Page/SlicerCommunity/2011-2014 - Revision history

Marianna at 20:10, 11 February 2020

2020-02-11T20:10:12Z

Marianna at 17:01, 11 February 2020

2020-02-11T17:01:17Z

Marianna: /* Cardiovascular Magnetic Resonance Imaging of Scar Development Following Pulmonary Vein Isolation: A Prospective Study */

2020-02-10T17:42:52Z

Cardiovascular Magnetic Resonance Imaging of Scar Development Following Pulmonary Vein Isolation: A Prospective Study

Marianna: /* Bi-modal Non-rigid Registration of Brain MRI Data with Deconvolution of Joint Statistics */

2020-02-10T17:42:33Z

Bi-modal Non-rigid Registration of Brain MRI Data with Deconvolution of Joint Statistics

Grundlett: Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:12:14Z

Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Marianna: /* SARRP Dose Planning System */

2019-03-12T19:43:21Z

SARRP Dose Planning System

Marianna: /* Talairach Methodology in the Multimodal Imaging and Robotics Era */

2019-03-12T19:41:16Z

Talairach Methodology in the Multimodal Imaging and Robotics Era

Marianna: /* SARRP Dose Planning System */

2019-03-12T19:40:46Z

SARRP Dose Planning System

Marianna: /* Talairach Methodology in the Multimodal Imaging and Robotics Era */

2019-03-04T16:35:57Z

Talairach Methodology in the Multimodal Imaging and Robotics Era

Marianna: /* Talairach Methodology in the Multimodal Imaging and Robotics Era */

2019-03-04T16:28:55Z

Talairach Methodology in the Multimodal Imaging and Robotics Era

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-Go to <big>[https://www.slicer.org/wiki/Main_Page/SlicerCommunity 2017] ::  [https://www.slicer.org/wiki/Main_Page/SlicerCommunity-2016 2016]:: [[Main_Page/SlicerCommunity-2015|2015]] :: [[Main_Page/SlicerCommunity-2011-2014|2014-2011]] :: [[Main_Page/SlicerCommunity-2005-2010|2010-2005]]</big>
+Go to <big>[https://www.slicer.org/wiki/Main_Page/SlicerCommunity/2020 2020] ::  [https://www.slicer.org/wiki/Main_Page/SlicerCommunity/2019 2019]  ::
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-'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/24663245 PLoS One. 2014 Mar 24;9(3):e92862. PMID: 24663245]| [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963974/pdf/pone.0092862.pdf PDF]
+'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/24663245 PLoS One. 2014 Mar 24;9(3):e92862. PMID: 24663245] | [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963974/pdf/pone.0092862.pdf PDF]
 '''Authors:''' Konishi J, Asami T, Hayano F, Yoshimi A, Hayasaka S, Fukushima H, Whitford TJ, Inoue T, Hirayasu Y.
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-'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/23490279 BJU Int. 2013 Nov;112(7):898-904. PMID: 23490279]| [http://onlinelibrary.wiley.com/doi/10.1111/bju.12024/epdf PDF]
+'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/23490279 BJU Int. 2013 Nov;112(7):898-904. PMID: 23490279] | [http://onlinelibrary.wiley.com/doi/10.1111/bju.12024/epdf PDF]
 '''Authors:''' Kanao K, Eastham JA, Scardino PT, Reuter VE, Fine SW.
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-'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/24130724 PLoS One. 2013 Oct 10;8(10):e75602. PMID: 24130724]| [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3794958/pdf/pone.0075602.pdf PDF]
+'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/24130724 PLoS One. 2013 Oct 10;8(10):e75602. PMID: 24130724] | [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3794958/pdf/pone.0075602.pdf PDF]
 '''Authors:''' Kim HJ, Kim J, Cho H, Ye BS, Yoon CW, Noh Y, Kim GH, Lee JH, Kim JS, Choe YS, Lee KH, Kim CH, Seo SW, Weiner MW, Na DL, Seong JK.
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-'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/24039922 PLoS One. 2013 Sep 6;8(9):e73353. PMID: 24039922]| [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765204 PDF]
+'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/24039922 PLoS One. 2013 Sep 6;8(9):e73353. PMID: 24039922] | [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765204 PDF]
 '''Authors:''' De Witt Hamer PC, Hendriks EJ, Mandonnet E, Barkhof F, Zwinderman AH, Duffau H.
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-'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/240864754 PLoS One. 2013 Sep 24;8(9):e75237. PMID: 24086475]| [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3782467 PDF]
+'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/240864754 PLoS One. 2013 Sep 24;8(9):e75237. PMID: 24086475] | [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3782467 PDF]
 '''Authors:''' Wampole ME, Kairys JC, Mitchell EP, Ankeny ML, Thakur ML, Wickstrom E.
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-'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/22878006 AJNR Am J Neuroradiol. 2013 Mar;34(3):622-7. PMID: 22878006]| [http://www.ajnr.org/content/34/3/622.full.pdf+html PDF]
+'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/22878006 AJNR Am J Neuroradiol. 2013 Mar;34(3):622-7. PMID: 22878006] | [http://www.ajnr.org/content/34/3/622.full.pdf+html PDF]
 '''Authors:''' Elias EJ, Liao JH, Jara H, Watanabe M, Nadgir RN, Sakai Y, Erbay K, Saito N, Ozonoff A, Steinberg MH, Sakai O.
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-'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/22075059 Am J Obstet Gynecol. 2012 Mar;206(3):244.e1-9. PMID: 22075059] |[[media:Rodrigues-AmJObstetGynecol2011.pdf | PDF]]
+'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/22075059 Am J Obstet Gynecol. 2012 Mar;206(3):244.e1-9. PMID: 22075059] | [[media:Rodrigues-AmJObstetGynecol2011.pdf | PDF]]
 '''Authors:''' Rodrigues AA Jr, Bassaly R, McCullough M, Terwilliger HL, Hart S, Downes K, Hoyte L.

← Older revision		Revision as of 17:42, 10 February 2020
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	\|align="right"\|[[image:Hsing-PLosOne2014-fig3.png\|thumb\|300px\| 16 segment model showing the 4 regions evaluated around each pulmonary vein. A) Zoomed and cropped slices labeled by region. B) 3D color-coded display, showing 4 regions about each PV, with explicit labeling for the right inferior and left superior PV. Image analyses were performed using ImageJ (NIH Image, Bethesda, MD) and [http://slicer.org '''3D Slicer'''] (v3.6, NA-MIC, Boston, MA).]]		\|align="right"\|[[image:Hsing-PLosOne2014-fig3.png\|thumb\|300px\| 16 segment model showing the 4 regions evaluated around each pulmonary vein. A) Zoomed and cropped slices labeled by region. B) 3D color-coded display, showing 4 regions about each PV, with explicit labeling for the right inferior and left superior PV. Image analyses were performed using ImageJ (NIH Image, Bethesda, MD) and [http://slicer.org '''3D Slicer'''] (v3.6, NA-MIC, Boston, MA).]]
		+	\|}
		+
		+	==Bi-modal Non-rigid Registration of Brain MRI Data with Deconvolution of Joint Statistics==
		+	{\|width="100%"
		+	\|
		+	'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/25020093 IEEE Trans Image Process. 2014 Sep;23(9):3999-4009. PMID: 25020093]
		+
		+	'''Authors:''' Pilutti D, Strumia M, Hadjidemetriou S.
		+
		+	'''Institution:''' Department of Radiology Medical Physics, University Medical Center Freiburg, Freiburg, Germany.
		+
		+	'''Background/Purpose:''' A brain MRI protocol typically includes several imaging contrasts that can provide complementary information by highlighting different tissue properties. The acquired data sets often need to be coregistered or placed in a standard anatomic space before any further processing. Current registration methods particularly for multicontrast data are computationally very intensive, their resolution is lower than that of the images, and their distance metric and its optimization can be limiting. In this paper, a novel and effective nonrigid registration method is proposed that is based on the restoration of the joint statistics of pairs of such images. The registration is performed with the deconvolution of the joint statistics with an adaptive Wiener filter. The deconvolved statistics are forced back to the spatial domain to estimate a preliminary registration. The spatial transformation is also regularized with Gaussian spatial smoothing. The registration method has been compared with the B-Splines method implemented in [http://slicer.org '''3D Slicer'''] and with the SyN method implemented in the ANTs toolkit. The validation has been performed with a simulated Shepp–Logan phantom, a BrainWeb phantom, the real data of the NIREP database, and real multicontrast data sets of healthy volunteers. The proposed method has shown improved comparative accuracy as well as analytical efficiency.
	\|}		\|}

← Older revision		Revision as of 17:42, 10 February 2020
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	'''Background/Purpose:''' Spontaneous intracerebral hemorrhage (ICH) can be devastating, particularly if hematoma expansion (HE) occurs. Tranexamic acid (TA), an antifibrinolytic drug, significantly reduced mortality in bleeding patients after trauma in the large CRASH-2 trial. The CRASH-2 ICH substudy found that TA nonsignificantly reduced mortality and dependency in traumatic ICH. The aim of this study was to assess the feasibility of performing a randomized controlled trial of tranexamic acid in spontaneous ICH, ahead of a definitive study. Methods: We performed a single-center, prospective, randomized (2:1), double-blind, placebo-controlled blinded endpoint trial of TA (intravenous 1 g bolus, 1 g infusion/8 h) in acute (<24 hours) spontaneous ICH. The primary objective was to test the feasibility of recruiting to the trial. Other objectives included tolerability (adverse events) and the effect of TA on HE and death and dependency. Results: The trial was feasible, with 24 patients enrolled (TA, n=16; placebo, n=8) between March 2011 and March 2012, and acceptable-only 3 patients declined to participate. All patients received the correct randomized treatment; 1 patient in the TA group did not complete the infusion because of neurologic deterioration. There were no significant differences in secondary outcomes including adverse events, HE, death, and dependency. One patient in the TA group had a deep vein thrombosis. Conclusions: This, the first randomized controlled trial of TA in ICH, found that the protocol could be delivered on schedule (2 patients/mo) and was feasible. Larger studies are needed to assess safety and efficacy of TA in ICH. The data were converted to analyze format before volumetric analysis using [http://slicer.org '''3D Slicer'''] software.		'''Background/Purpose:''' Spontaneous intracerebral hemorrhage (ICH) can be devastating, particularly if hematoma expansion (HE) occurs. Tranexamic acid (TA), an antifibrinolytic drug, significantly reduced mortality in bleeding patients after trauma in the large CRASH-2 trial. The CRASH-2 ICH substudy found that TA nonsignificantly reduced mortality and dependency in traumatic ICH. The aim of this study was to assess the feasibility of performing a randomized controlled trial of tranexamic acid in spontaneous ICH, ahead of a definitive study. Methods: We performed a single-center, prospective, randomized (2:1), double-blind, placebo-controlled blinded endpoint trial of TA (intravenous 1 g bolus, 1 g infusion/8 h) in acute (<24 hours) spontaneous ICH. The primary objective was to test the feasibility of recruiting to the trial. Other objectives included tolerability (adverse events) and the effect of TA on HE and death and dependency. Results: The trial was feasible, with 24 patients enrolled (TA, n=16; placebo, n=8) between March 2011 and March 2012, and acceptable-only 3 patients declined to participate. All patients received the correct randomized treatment; 1 patient in the TA group did not complete the infusion because of neurologic deterioration. There were no significant differences in secondary outcomes including adverse events, HE, death, and dependency. One patient in the TA group had a deep vein thrombosis. Conclusions: This, the first randomized controlled trial of TA in ICH, found that the protocol could be delivered on schedule (2 patients/mo) and was feasible. Larger studies are needed to assess safety and efficacy of TA in ICH. The data were converted to analyze format before volumetric analysis using [http://slicer.org '''3D Slicer'''] software.
−	\|}
−
−	~~==Bi-modal Non-rigid Registration of Brain MRI Data with Deconvolution of Joint Statistics==~~
−	~~{\|width="100%"~~
−	\|
−	~~'''Publication:''' [http://www.ncbi.nlm.nih.gov/pubmed/25020093 IEEE Trans Image Process. 2014 Jul 8. PMID: 25020093]~~
−
−	~~'''Authors:''' Pilutti D, Strumia M, Hadjidemetriou S.~~
−
−	~~'''Institution:''' Department of Radiology Medical Physics, University Medical Center Freiburg, Freiburg, Germany.~~
−
−	'''Background/Purpose:''' A brain MRI protocol typically includes several imaging contrasts that can provide complementary information by highlighting different tissue properties. The acquired data sets often need to be coregistered or placed in a standard anatomic space before any further processing. Current registration methods particularly for multicontrast data are computationally very intensive, their resolution is lower than that of the images, and their distance metric and its optimization can be limiting. In this paper, a novel and effective nonrigid registration method is proposed that is based on the restoration of the joint statistics of pairs of such images. The registration is performed with the deconvolution of the joint statistics with an adaptive Wiener filter. The deconvolved statistics are forced back to the spatial domain to estimate a preliminary registration. The spatial transformation is also regularized with Gaussian spatial smoothing. The registration method has been compared with the B-Splines method implemented in [http://slicer.org '''3D Slicer'''] and with the SyN method implemented in the ANTs toolkit. The validation has been performed with a simulated Shepp–Logan phantom, a BrainWeb phantom, the real data of the NIREP database, and real multicontrast data sets of healthy volunteers. The proposed method has shown improved comparative accuracy as well as analytical efficiency.
	\|}		\|}

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-Go to <big>[https://www.slicer.org/wiki/Main_Page/SlicerCommunity 2017] ::  [https://www.slicer.org/wiki/Main_Page/SlicerCommunity-2016 2016]:: [http://wiki.slicer.org/slicerWiki/index.php/Main_Page/SlicerCommunity-2015 2015] :: [http://wiki.slicer.org/slicerWiki/index.php/Main_Page/SlicerCommunity-2011-2014 2014-2011] :: [http://wiki.slicer.org/slicerWiki/index.php/Main_Page/SlicerCommunity-2005-2010 2010-2005]</big>
+Go to <big>[https://www.slicer.org/wiki/Main_Page/SlicerCommunity 2017] ::  [https://www.slicer.org/wiki/Main_Page/SlicerCommunity-2016 2016]:: [[Main_Page/SlicerCommunity-2015|2015]] :: [[Main_Page/SlicerCommunity-2011-2014|2014-2011]] :: [[Main_Page/SlicerCommunity-2005-2010|2010-2005]]</big>
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-'''Company:''' [https://xstrahl.com/life-science-systems/small-animal-radiation-research-platform/  Xstrahl Ltd.], Camberley, UK.
+'''Company:''' [https://xstrahl.com Xstrahl Ltd.], Camberley, UK.
-'''Background:''' The SARRP dose planning system (DPS) is a dedicated in vivo treatment planning system designed to calculate dose distributions in pre-clinical radiation studies. The SARRP DPS is specifically validated for use with in vivo—uniquely enabling the user to treat very precise areas of the animal by defining the area and visualizing the dose and as a result, enabling a more accurate experiment and final result. [http://www.xstrahl.com/planningsystems.htm More...]
+'''Background:''' The SARRP dose planning system (DPS) is a dedicated in vivo treatment planning system designed to calculate dose distributions in pre-clinical radiation studies. The SARRP DPS is specifically validated for use with in vivo—uniquely enabling the user to treat very precise areas of the animal by defining the area and visualizing the dose and as a result, enabling a more accurate experiment and final result. [https://xstrahl.com/life-science-systems/small-animal-radiation-research-platform/  More...]
 |align="right"|[[image:DosePlanning_Cycle3.jpg|300px|thumb|Dose Planning System]]

@@ Line 1,668: / Line 1,668: @@
 '''Background/Purpose:''' The original Talairach methodology was based on three main features. Neuroimaging techniques to collect patient-specific brain anatomical data, a probabilistic morpho-functional atlas and surgical tools developed to implant intracerebral electrodes in accurate and safe conditions. Brain anatomy was obtained indirectly by means of cerebral angiography and ventriculography. Both techniques were performed in stereotactic (coordinate system), telemetric (reduced magnification and distortion) and stereoscopic (pseudo-3D effect) conditions. The following step was to normalize patient’s specific data to the atlas space using the bicommissural coordinate system. The normalization to the atlas was fundamental in order to integrate the images with structural (gyri and sulci), cytoarchitectural (Brodmann areas) and functional (electrical stimulations) data. Then, in order to position the guiding screws along the pre-planned trajectory, a double grid was attached onto the frame, allowing drilling in the orthogonal direction. Nowadays modern technological tools facilitate the workflow, but the main concepts of this methodology are still valid. We use algorithms completely automated with software applications to expand the multimodal integration of data so that MRI, rotational angiography, fMRI and DTI-FT data can all be coregistered together. It is now possible to obtain real 3D viewing by multi-planar reconstructions (MPR), volume and surface rendering. The tool holder for the surgical implantation is now fixed onto the passive robotic arm of the stereotactic image-guided system Renishaw neuromate®, so that the number of possible trajectories is no more discrete (as using the double grid), but virtually infinite with any desired obliquity. The aim of this chapter is to describe our present workflow. We will underline the methodological continuity with basic Talairach and Bancaud principles, highlighting how modern tools can help in saving time and improve safety, accuracy and the amount of information. Moreover, we report our quantitative results regarding geometrical accuracy at the cortical entry point with this new methodology.
-|align="right"|[[image:Cardinale-SEEG_Scarabin2012.png|300px|thumb|[http://www.slicer.org/ '''3D Slicer'''] scene with MPR and 3D views (crossed viewing) During long-term Video-SEEGmonitoring, for several days following implantation, it is important to have intuitive and accurate mapping tools for localizing the sources of the signal. In order to reach this aim, we integrate all the information in [http://www.slicer.org/ '''3D Slicer'''], a package able to load all data. It is in fact possible to import all datasets and surface models computed by FreeSurfer (white and gray matter, with parcellations and labels). Moreover, it is possible to create other models such as the vascular tree and the electrodes leads. This is done very simply with the Gray Scale Model Maker tool. [http://slicer.org '''3D Slicer'''] is installed on all team members’ computers, so that epileptologists are able to look at these scenes when interpreting the SEEG traces. (A and B) constitute a pair of stereoscopic images with the reconstruction of pial surface, vessels and labeled electrodes. (C, D and E) are the MPR views, with the visualization fading 50% for MRI and 50% for post-implant O-arm dataset. The crosshair indicates the second lead of an electrode exploring first temporal gyrus,temporal transverse gyri and insular long gyri.]]
+|align="right"|[[image:Cardinale-SEEG_Scarabin2012.png|300px|thumb|[http://www.slicer.org/ '''3D Slicer'''] scene with MPR and 3D views (crossed viewing) During long-term Video-SEEGmonitoring, for several days following implantation, it is important to have intuitive and accurate mapping tools for localizing the sources of the signal. In order to reach this aim, we integrate all the information in [http://www.slicer.org/ '''3D Slicer'''], a package able to load all data. It is in fact possible to import all datasets and surface models computed by FreeSurfer (white and gray matter, with parcellations and labels). Moreover, it is possible to create other models such as the vascular tree and the electrodes leads. This is done very simply with the Gray Scale Model Maker tool. [http://slicer.org '''3D Slicer'''] is installed on all team members’ computers, so that epileptologists are able to look at these scenes when interpreting the SEEG traces. (A and B) constitute a pair of stereoscopic images with the reconstruction of pial surface, vessels and labeled electrodes. (C, D and E) are the MPR views, with the visualization fading 50% for MRI and 50% for post-implant O-arm dataset. The crosshair indicates the second lead of an electrode exploring first temporal gyrus, temporal transverse gyri and insular long gyri.]]
 |}

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-'''Publication:''' Book Chapter in: Jean-Marie Scarabin Ed. Stereotaxy and Epilepsy Surgery. John Libbey Eurotext LTD. 2012 Sep; p.245-72. ISBN-10: 2742007679. [[media:Cardinale-Scarabin_SEEG-2.pdf | PDF]]
+'''Publication:''' Book Chapter in: Jean-Marie Scarabin Ed. Stereotaxy and Epilepsy Surgery. John Libbey Eurotext LTD. 2012 Sep; p.245-72. ISBN-10: 2742007679.
 '''Authors:''' Cardinale F, Miserocchi A, Moscato A, Cossu M, Castana L, Schiariti M P, Gozzo F, Pero G, Quilici L, Citterio A, Minella M, Torresin A, Lo Russo G.