https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=Fischl 2026-04-24T00:31:11Z User contributions MediaWiki 1.33.0 https://www.na-mic.org/w/index.php?title=2008_Progress_Report_NIH_QnA&diff=28465 2008-07-24T18:40:31Z

<p>Fischl: /* MGH Response (Bruce Fischl) */</p> <hr /> <div>=Please address promptly (by July 30th, 5pm)=<br /> <br /> =MGH=<br /> *What progress has been made with the MGH subcontract in the past year?<br /> **There's no progress report summary following the Statement of Intent for MGH (page 42). We recognize that MGH's budget was significantly reduced this past year, as a good portion was re-budgeted to Washington University beginning in December 2007. Nevertheless, we expect some progress to have been made.<br /> **The scientific progress report lists MGH as participating in some efforts (Shape Based Segmentation and Registration; Spherical Wavelets; and Shape Analysis with Overcomplete Wavelets), but there are no MGH personnel listed as key investigators for that section.<br /> *With regard to future work (Dr. Fischl's consultation), the statement of work refers to &quot;integration of FreeSurfer with ITK and 3D Slicer.&quot; What does that mean? Wasn't that effort abandoned.<br /> *The progress report is somewhat confusing as to whether FreeSurfer is being used to study cortical correspondence. On page 250 (Section 3.2) a collaboration between MGH and MIT is mentioned with respect to cortical correspondence, while the UNC progress report states that MOL is being used to explore cortical correspondence. Please clarify.<br /> ==MGH Response ('''Bruce Fischl''')==<br /> <br /> The overcomplete wavelet project has resulted in a conference publication, and we are actively working on it's completion. We are currently working on incorporating geometric invariants to replace the coordinate functions, and also on augmenting our existing neonate datasets with one or two more manually labeled cases so that we can assess how well our model fits the data.<br /> <br /> Going forward we intend to improve the FreeSurfer/Slicer/ITK interoperability. Towards this end we have worked with Core 2 to incorporate support for our internal formats in Slicer, and intend to include support for ITK formats such as NRRD directly into FreeSurfer. This will significantly increase the ease of development of algorithms that take advantage of the two platforms.<br /> <br /> <br /> We also have an ongoing collaboration with Drs. Polina Golland, Mert Sabuncu and Thomas Yeo at MIT regarding improving cortical correspondence. Specifically, the existing FreeSurfer algorithms are being used to generate a baseline state-of-the-art accuracy measure that will be used to assess the performance of novel registration algorithms. Here we are working on both fast diffeormophic registration, and have a recent conference paper describing the &quot;spherical demons&quot; algorithm that improves execution time significantly without sacrificing performance. In addition, we as part of Mr. Yeo's Ph.D. research we are developing techniques for the optimal alignment of either archectonically or functionally defined cortical regions, defined using whole-brain histology and functional MRI respectively.<br /> <br /> =UCLA=<br /> <br /> *What progress has been made with the UCLA subcontract in the past year?<br /> **There are no publications listed in progress report. A search of NA-MIC publications database shows only one paper with Art Toga or Nathan Hageman's name on it, and that's the iTools paper (from the Software and Data Integration Working Group).<br /> **Timeline information is out of date. It has not been updated to reflect the changes in the statement of work that was agreed upon in August 2007.<br /> ==UCLA Response ('''Arthur Toga''')==<br /> <br /> =Queens=<br /> *Regarding the Brachytherapy Needle Positioning Robot Integration DBP:<br /> **Which grant is funding the patient data collection? If it is supported by NA-MIC, please let me know because NIBIB will have to approve your Data Safety Monitoring Plan.<br /> **There seems to be some scientific overlap between this project and other NIH-funded grants, R01 EB002963 (PI: Whitcomb [previously Fichtinger]) and R01 CA111288 (PI:Tempany). The statement of work for the NA-MIC subcontract states, &quot;The deliverables of the contract is professional-grade clinical software engineering of the above modules based on the NA-MIC toolkit (to the extent reasonable and possible) and to develop end applications based on Slicer, for clinical trials in image-gu ided prostate biopsy.&quot; However, this goal also falls within the System Integration aim (Aim 3) of the NCI grant and the System Integration aim (Aim 3) of the NIBIB grant. Please provide us with additional clarification to distinguish these projects in terms of their aims. Also, please confirm that Dr. Gobbi and Mr. Vikal are being supported at no more than 3 and 6 months, respectively by other grants (as they are listed for 9 and 6 months on the NAMIC subcontract).<br /> ==Queens Response ('''Gabor Fichtinger''')==<br /> <br /> =Kitware=<br /> *Kitware is working on a text, &quot;Practical Software Process&quot;, to document the NA-MIC software process. How will that be distributed? Will NA-MIC funds cover all the costs so that the text can be distributed free of charge?<br /> ==Kitware Response ('''Will Schroeder''')==<br /> <br /> =Dissemination Core=<br /> *What does it mean when you say that you NA-MIC hosted the Workshop on Open Source and Open Data at MICCAI 2007? Did NA-MIC providing financial support? Set the agenda? Invite participants? Please clarify.<br /> ==Dissemination Core Response ('''Tina Kapur''')==<br /> NA-MIC personnel contributed their time to conduct typical tasks involved in chairing a workshop such as soliciting manuscripts and open reviews, setting the agenda, and inviting speakers for keynote presentations. No financial support was needed or provided by NA-MIC other than travel of NA-MIC presenters to the conference.<br /> <br /> <br /> <br /> <br /> <br /> <br /> =Questions for non-urgent consideration:=<br /> ==MIND==<br /> *Systemic Lupus Erythematous project<br /> **Has this project driven any new algorithm development?<br /> **Have the new tools been tested on other lesions? What other sorts of lesions are likely to benefit from them?<br /> **Has manual segmentation (which is serving as the gold standard for this project) been shown to have low inter-observer variability?<br /> ===Mind Response ('''Jeremy Bockholt''')===<br /> <br /> ==Structural Image Analysis==<br /> *Is NA-MIC supporting the UNC-Ied (Martin Styner) 3D Segmentation in the Clinic Workshop at MICCAI 2008? If so, in what ways?<br /> *Does NA-MIC have any process planned for eliminating an algorithm from its toolkit if a competing algorithm outperforms it?<br /> *Are there any plans to integrate results from the segmentation workshop into documentation for Slicer in such a way that they are readily accessible to users choosing between Slicer modules?<br /> ===Structural Image Analysis Response ('''Martin Styner with input from other Core 1 and 2 people''')===<br /> <br /> '''Response (to #2 above):''' NA-MIC is the provider of a research software platform. We do not believe that eliminating algorithms from the NA-MIC kit is in the best interest of the research community because even if a particular algorithm is not actively used as part of an end-to-end clinical solution today, or does not perform as well as another one in the context of a particular task, we want to remain open to the possibility that it could be a key enabler of solutions in the future. However, for algorithms that are part of end-to-end solutions to problems that we are actively working on, we are making a concerted effort to provide publicly accessible tutorial materials to explain and encourage their adoption.<br /> <br /> ==Miscellaneous==<br /> ===Kitware ('''Will Schroeder''')===<br /> Some concerns were raised regarding the blurring of the distinction between NA-MIC, ITK and VTK. We recognize the contributions that NA-MIC-funded programmers have made to both ITK and VTK and we recognize that the relationship between NA-MIC and the other toolkits is beneficial to a broad development and user community. However, in some cases there seems to be insufficient acknowledgement in the report of the tools that predated NAMIC and helped lay the groundwork for it; for example CMake and DART.<br /> ===St. Louis ('''Dan Marcus''')===<br /> XNAT is open-source using the XNAT License . What does that mean? Is it different than the NA-MIC license?<br /> ===Isomics ('''Steve Pieper''')===<br /> Isomics' statement of work states: Significant effort will be devoted to re-architecting core components of 3D Slicer to make them better interoperate with other NA-MIC tools. Wasn't Slicer developed in parallel with NA-MIC tools? How have incompatibilities arisen?<br /> <br /> Response: Version 2.x of 3D Slicer existed for a number of years prior to NA-MIC and is still used by NA-MIC participants for specific tasks. Development of version 3.x is now about 2 years old and has been developed with NA-MIC tools as the foundation. A number of functional blocks continue to be ported and re-architected to leverage the new environment. Examples include the interactive diffusion imaging modules, the Label Map Editor, and the Image Guided Therapy interfaces. In addition, as new functionality such as XNAT and Grid Wizard are added to the NA-MIC Kit, new interfaces are required.<br /> <br /> ===UCSD ('''Jeff Grethe''')===<br /> The report includes no specific information on progress at UCSD in developing and supporting grid computing for NA-MIC.<br /> ===Training Core ('''Randy Gollub''')===<br /> Please tell us a bit more about the training core's program to provide one-on-one mentoring (it's mentioned in the timeline , but there's no information on the Wiki). How is it structured? Who can be mentored? How does one arrange for mentorship?<br /> ===Some updates to the timeline are needed:===<br /> ====Bruce Fischl====<br /> The timeline for MGH indicates that many of the tasks have been modified, but these modifications aren't listed in the table of timeline modifications.<br /> ====Dan Marcus====<br /> Why not list Wash U in the timeline for the appropriate tasks?<br /> ====Ross Whitaker====<br /> Certain tasks have been removed from the Utah aims because they have been &quot;subsumed by Core 1-2 partners&quot;, presumably MGH. Now that the plans have changed so that MGH no longer plans to do this work, this needs to be updated.<br /> ====Will Schroeder====<br /> *Has there been progress in the migration from LONI to batchmake? It is not yet listed as complete in the Isomics timeline.<br /> *Based on the timeline, Kitware has completed its tasks . Some new tasks are listed in the statement of work and should be entered into the timeline.<br /> ====Tina Kapur====<br /> For the future (assuming and hoping there is a future!) , it would be nice to have publications listed at the end of each relevant section (in addition to the Additional Information links currently provided). Several members of the Center team commented on the lack of details in the progress report and wanted to follow up by reading the relevant publications.<br /> <br /> '''Response:''' Thanks for the suggestion. We will follow it in the future.</div>

Fischl https://www.na-mic.org/w/index.php?title=2008_Progress_Report_NIH_QnA&diff=28464 2008-07-24T18:22:30Z

<p>Fischl: /* MGH Response (Bruce Fischl) */</p> <hr /> <div>=Please address promptly (by July 30th, 5pm)=<br /> <br /> =MGH=<br /> *What progress has been made with the MGH subcontract in the past year?<br /> **There's no progress report summary following the Statement of Intent for MGH (page 42). We recognize that MGH's budget was significantly reduced this past year, as a good portion was re-budgeted to Washington University beginning in December 2007. Nevertheless, we expect some progress to have been made.<br /> **The scientific progress report lists MGH as participating in some efforts (Shape Based Segmentation and Registration; Spherical Wavelets; and Shape Analysis with Overcomplete Wavelets), but there are no MGH personnel listed as key investigators for that section.<br /> *With regard to future work (Dr. Fischl's consultation), the statement of work refers to &quot;integration of FreeSurfer with ITK and 3D Slicer.&quot; What does that mean? Wasn't that effort abandoned.<br /> *The progress report is somewhat confusing as to whether FreeSurfer is being used to study cortical correspondence. On page 250 (Section 3.2) a collaboration between MGH and MIT is mentioned with respect to cortical correspondence, while the UNC progress report states that MOL is being used to explore cortical correspondence. Please clarify.<br /> ==MGH Response ('''Bruce Fischl''')==<br /> <br /> The overcomplete wavelet project has resulted in a conference publication, and we are actively working on it's completion. We anticipate handing the code off to core 2 for inclusion in ITK in the next 12 months.<br /> <br /> Going forward we intend to improve the FreeSurfer/Slicer/ITK interoperability. Towards this end we have worked with Core 2 to incorporate support for our internal formats in Slicer, and intend to include support for ITK formats such as NRRD directly into FreeSurfer. This will significantly increase the ease of development of algorithms that take advantage of the two platforms.<br /> <br /> <br /> We also have an ongoing collaboration with Drs. Polina Golland, Mert Sabuncu and Thomas Yeo at MIT regarding improving cortical correspondence. Specifically, the existing FreeSurfer algorithms are being used to generate a baseline state-of-the-art accuracy measure that will be used to assess the performance of novel registration algorithms. Here we are working on both fast diffeormophic registration, and have a recent conference paper describing the &quot;spherical demons&quot; algorithm that improves execution time significantly without sacrificing performance. In addition, we as part of Mr. Yeo's Ph.D. research we are developing techniques for the optimal alignment of either archectonically or functionally defined cortical regions, defined using whole-brain histology and functional MRI respectively. All code developed in this research will be made available to Core 2 for future inclusion in ITK.<br /> <br /> =UCLA=<br /> <br /> *What progress has been made with the UCLA subcontract in the past year?<br /> **There are no publications listed in progress report. A search of NA-MIC publications database shows only one paper with Art Toga or Nathan Hageman's name on it, and that's the iTools paper (from the Software and Data Integration Working Group).<br /> **Timeline information is out of date. It has not been updated to reflect the changes in the statement of work that was agreed upon in August 2007.<br /> ==UCLA Response ('''Arthur Toga''')==<br /> <br /> =Queens=<br /> *Regarding the Brachytherapy Needle Positioning Robot Integration DBP:<br /> **Which grant is funding the patient data collection? If it is supported by NA-MIC, please let me know because NIBIB will have to approve your Data Safety Monitoring Plan.<br /> **There seems to be some scientific overlap between this project and other NIH-funded grants, R01 EB002963 (PI: Whitcomb [previously Fichtinger]) and R01 CA111288 (PI:Tempany). The statement of work for the NA-MIC subcontract states, &quot;The deliverables of the contract is professional-grade clinical software engineering of the above modules based on the NA-MIC toolkit (to the extent reasonable and possible) and to develop end applications based on Slicer, for clinical trials in image-gu ided prostate biopsy.&quot; However, this goal also falls within the System Integration aim (Aim 3) of the NCI grant and the System Integration aim (Aim 3) of the NIBIB grant. Please provide us with additional clarification to distinguish these projects in terms of their aims. Also, please confirm that Dr. Gobbi and Mr. Vikal are being supported at no more than 3 and 6 months, respectively by other grants (as they are listed for 9 and 6 months on the NAMIC subcontract).<br /> ==Queens Response ('''Gabor Fichtinger''')==<br /> <br /> =Kitware=<br /> *Kitware is working on a text, &quot;Practical Software Process&quot;, to document the NA-MIC software process. How will that be distributed? Will NA-MIC funds cover all the costs so that the text can be distributed free of charge?<br /> ==Kitware Response ('''Will Schroeder''')==<br /> <br /> =Dissemination Core=<br /> *What does it mean when you say that you NA-MIC hosted the Workshop on Open Source and Open Data at MICCAI 2007? Did NA-MIC providing financial support? Set the agenda? Invite participants? Please clarify.<br /> ==Dissemination Core Response ('''Tina Kapur''')==<br /> NA-MIC personnel contributed their time to conduct typical tasks involved in chairing a workshop such as soliciting manuscripts and open reviews, setting the agenda, and inviting speakers for keynote presentations. No financial support was needed or provided by NA-MIC other than travel of NA-MIC presenters to the conference.<br /> <br /> <br /> <br /> <br /> <br /> <br /> =Questions for non-urgent consideration:=<br /> ==MIND==<br /> *Systemic Lupus Erythematous project<br /> **Has this project driven any new algorithm development?<br /> **Have the new tools been tested on other lesions? What other sorts of lesions are likely to benefit from them?<br /> **Has manual segmentation (which is serving as the gold standard for this project) been shown to have low inter-observer variability?<br /> ===Mind Response ('''Jeremy Bockholt''')===<br /> <br /> ==Structural Image Analysis==<br /> *Is NA-MIC supporting the UNC-Ied (Martin Styner) 3D Segmentation in the Clinic Workshop at MICCAI 2008? If so, in what ways?<br /> *Does NA-MIC have any process planned for eliminating an algorithm from its toolkit if a competing algorithm outperforms it?<br /> *Are there any plans to integrate results from the segmentation workshop into documentation for Slicer in such a way that they are readily accessible to users choosing between Slicer modules?<br /> ===Structural Image Analysis Response ('''Martin Styner with input from other Core 1 and 2 people''')===<br /> <br /> '''Response (to #2 above):''' NA-MIC is the provider of a research software platform. We do not believe that eliminating algorithms from the NA-MIC kit is in the best interest of the research community because even if a particular algorithm is not actively used as part of an end-to-end clinical solution today, or does not perform as well as another one in the context of a particular task, we want to remain open to the possibility that it could be a key enabler of solutions in the future. However, for algorithms that are part of end-to-end solutions to problems that we are actively working on, we are making a concerted effort to provide publicly accessible tutorial materials to explain and encourage their adoption.<br /> <br /> ==Miscellaneous==<br /> ===Kitware ('''Will Schroeder''')===<br /> Some concerns were raised regarding the blurring of the distinction between NA-MIC, ITK and VTK. We recognize the contributions that NA-MIC-funded programmers have made to both ITK and VTK and we recognize that the relationship between NA-MIC and the other toolkits is beneficial to a broad development and user community. However, in some cases there seems to be insufficient acknowledgement in the report of the tools that predated NAMIC and helped lay the groundwork for it; for example CMake and DART.<br /> ===St. Louis ('''Dan Marcus''')===<br /> XNAT is open-source using the XNAT License . What does that mean? Is it different than the NA-MIC license?<br /> ===Isomics ('''Steve Pieper''')===<br /> Isomics' statement of work states: Significant effort will be devoted to re-architecting core components of 3D Slicer to make them better interoperate with other NA-MIC tools. Wasn't Slicer developed in parallel with NA-MIC tools? How have incompatibilities arisen?<br /> <br /> Response: Version 2.x of 3D Slicer existed for a number of years prior to NA-MIC and is still used by NA-MIC participants for specific tasks. Development of version 3.x is now about 2 years old and has been developed with NA-MIC tools as the foundation. A number of functional blocks continue to be ported and re-architected to leverage the new environment. Examples include the interactive diffusion imaging modules, the Label Map Editor, and the Image Guided Therapy interfaces. In addition, as new functionality such as XNAT and Grid Wizard are added to the NA-MIC Kit, new interfaces are required.<br /> <br /> ===UCSD ('''Jeff Grethe''')===<br /> The report includes no specific information on progress at UCSD in developing and supporting grid computing for NA-MIC.<br /> ===Training Core ('''Randy Gollub''')===<br /> Please tell us a bit more about the training core's program to provide one-on-one mentoring (it's mentioned in the timeline , but there's no information on the Wiki). How is it structured? Who can be mentored? How does one arrange for mentorship?<br /> ===Some updates to the timeline are needed:===<br /> ====Bruce Fischl====<br /> The timeline for MGH indicates that many of the tasks have been modified, but these modifications aren't listed in the table of timeline modifications.<br /> ====Dan Marcus====<br /> Why not list Wash U in the timeline for the appropriate tasks?<br /> ====Ross Whitaker====<br /> Certain tasks have been removed from the Utah aims because they have been &quot;subsumed by Core 1-2 partners&quot;, presumably MGH. Now that the plans have changed so that MGH no longer plans to do this work, this needs to be updated.<br /> ====Will Schroeder====<br /> *Has there been progress in the migration from LONI to batchmake? It is not yet listed as complete in the Isomics timeline.<br /> *Based on the timeline, Kitware has completed its tasks . Some new tasks are listed in the statement of work and should be entered into the timeline.<br /> ====Tina Kapur====<br /> For the future (assuming and hoping there is a future!) , it would be nice to have publications listed at the end of each relevant section (in addition to the Additional Information links currently provided). Several members of the Center team commented on the lack of details in the progress report and wanted to follow up by reading the relevant publications.<br /> <br /> '''Response:''' Thanks for the suggestion. We will follow it in the future.</div>

Fischl https://www.na-mic.org/w/index.php?title=Projects:CorticalSurfaceShapeAnalysisUsingSphericalWavelets&diff=18373 2007-11-29T02:28:09Z

<p>Fischl: /* Cortical Surface Shape Analysis Based on Spherical Wavelets */</p> <hr /> <div>Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]], [[Algorithm:MGH|MGH Algorithms]]<br /> <br /> = Cortical Surface Shape Analysis Based on Spherical Wavelets =<br /> <br /> Cortical folding patterns vary both in terms of relative spatial location as well as in spatial frequency content. Wavelets are thus a natural tool for the analysis of folding patterns.<br /> <br /> = Description =<br /> <br /> ''Status'' Prototype<br /> <br /> ''Submitted'' IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> ''Abstract'' In vivo quantification of neuroanatomical shape variations is possible due to recent advances in medical imaging and has proven useful in the study of neuropathology and neurodevelopment. In this paper, we apply a spherical wavelet transformation to extract shape features of cortical surfaces reconstructed from<br /> magnetic resonance images (MRIs) of a set of subjects. The spherical wavelet transformation can characterize the underlying functions in a local fashion in both space and frequency, in contrast to spherical harmonics that have a global basis set. We perform principal component analysis (PCA) on these wavelet shape features to study patterns of shape variation within normal population from coarse to fine resolution. In addition, we study the development of cortical folding in newborns using the Gompertz model in the wavelet domain, which allows us to characterize the order of development of large-scale and finer folding patterns independently. Given a limited amount of training data, we use a regularization framework to estimate the parameters of the Gompertz model to improve the prediction performance on new data. We develop an efficient method to estimate this regularized Gompertz model based on the Broyden–Fletcher–Goldfarb–Shannon (BFGS) approximation. Promising results are presented using both PCA and the folding development model in the wavelet domain. The cortical folding development model provides quantitative anatomic information regarding macroscopic cortical folding development and may be of potential use as a biomarker for early diagnosis of neurologic deficits in newborns.<br /> <br /> = Key Investigators =<br /> <br /> * MGH: Peng Yu, P. Ellen Grant, Yuan Qi, Xiao Han, Florent Ségonne, Rudolph Pienaar, Evelina Busa, Jenni Pacheco, Nikos Makris, Randy L. Buckner, Polina Golland, and Bruce Fischl</div>

Fischl https://www.na-mic.org/w/index.php?title=Projects:NRDDFreesurfer&diff=18372 2007-11-29T02:26:02Z

<p>Fischl: /* Description */</p> <hr /> <div>Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]], [[Algorithm:MGH|MGH Algorithms]]<br /> <br /> = Adding NRRD I/O to Freesurfer =<br /> <br /> overview goes here<br /> <br /> = Description =<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Open a NRRD volume in FreeSurfer.' &lt;/nowiki&gt;<br /> * '''Use case'''&lt;nowiki&gt;: 'Convert an MGH volume to a NRRD volume with Freesurfer.' &lt;/nowiki&gt;<br /> * Difficulty: Low<br /> * Impact: Medium<br /> <br /> # Write unit tests for new IO functions (Snyder): '''completed'''<br /> # Add NrrdIO libraries from Teem to FS source tree, build with autoconf (Snyder): '''completed'''<br /> # Write and test FS NRRD IO functions (Snyder, Kindlmann): '''completed'''<br /> # Develop approriate headers for MGH DWI data (Teich): '''completed'''<br /> <br /> = Key Investigators =<br /> <br /> = Publications =<br /> <br /> = Links =</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18198 2007-11-28T14:15:26Z

<p>Fischl: /* Adding NRRD I/O to Freesurfer */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset.&lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:overcomplete_vs_biorthogonal_wavelets.tif|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. We propose a technique to accurately correct<br /> the spherical topology of cortical surfaces. Specifically,we construct<br /> a mapping from the original surface onto the sphere to detect<br /> topological defects as minimal nonhomeomorphic regions. The<br /> topology of each defect is then corrected by opening and sealing<br /> the surface along a set of nonseparating loops that are selected in<br /> a Bayesian framework. The proposed method is a wholly self-contained<br /> topology correction algorithm, which determines geometrically<br /> accurate, topologically correct solutions based on the magnetic<br /> resonance imaging (MRI) intensity profile and the expected<br /> local curvature. Applied to real data, our method provides topological<br /> corrections similar to those made by a trained operator.<br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:separating_loops.jpg|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. This project has been completed through the use of the open source packages VNL and Cephes. This includes the complete replacement of all Numerical Recipes in C code, and the implementation of a battery of unit tests for each replaced function. Currently the open source release is at a beta stage, and 10 beta releases of the source have been made. We anticipate a complete open source release in first quarter 2008.<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> [[Image:histo_matching.jpg|thumb|left|200px]]<br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18197 2007-11-28T14:14:52Z

<p>Fischl: /* Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset.&lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:overcomplete_vs_biorthogonal_wavelets.tif|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. We propose a technique to accurately correct<br /> the spherical topology of cortical surfaces. Specifically,we construct<br /> a mapping from the original surface onto the sphere to detect<br /> topological defects as minimal nonhomeomorphic regions. The<br /> topology of each defect is then corrected by opening and sealing<br /> the surface along a set of nonseparating loops that are selected in<br /> a Bayesian framework. The proposed method is a wholly self-contained<br /> topology correction algorithm, which determines geometrically<br /> accurate, topologically correct solutions based on the magnetic<br /> resonance imaging (MRI) intensity profile and the expected<br /> local curvature. Applied to real data, our method provides topological<br /> corrections similar to those made by a trained operator.<br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:separating_loops.jpg|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. This project has been completed through the use of the open source packages VNL and Cephes. This includes the complete replacement of all Numerical Recipes in C code, and the implementation of a battery of unit tests for each replaced function. Currently the open source release is at a beta stage, and 10 beta releases of the source have been made. We anticipate a complete open source release in first quarter 2008.<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> [[Image:histo_matching.jpg|thumb|left|200px]]<br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=File:Histo_matching.jpg&diff=18196 2007-11-28T14:13:28Z

<p>Fischl: Illustration of histogram matching. The plot shows the histogram for hippocampus built from the atlas and the input image respectively, and also the atlas histogram after the computed linear intensity mapping</p> <hr /> <div>Illustration of histogram matching. The plot shows the histogram for hippocampus built from the atlas and the input image respectively, and also the atlas histogram after the computed linear intensity mapping</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18195 2007-11-28T14:13:02Z

<p>Fischl: /* Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset.&lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:overcomplete_vs_biorthogonal_wavelets.tif|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. We propose a technique to accurately correct<br /> the spherical topology of cortical surfaces. Specifically,we construct<br /> a mapping from the original surface onto the sphere to detect<br /> topological defects as minimal nonhomeomorphic regions. The<br /> topology of each defect is then corrected by opening and sealing<br /> the surface along a set of nonseparating loops that are selected in<br /> a Bayesian framework. The proposed method is a wholly self-contained<br /> topology correction algorithm, which determines geometrically<br /> accurate, topologically correct solutions based on the magnetic<br /> resonance imaging (MRI) intensity profile and the expected<br /> local curvature. Applied to real data, our method provides topological<br /> corrections similar to those made by a trained operator.<br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:separating_loops.jpg|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. This project has been completed through the use of the open source packages VNL and Cephes. This includes the complete replacement of all Numerical Recipes in C code, and the implementation of a battery of unit tests for each replaced function. Currently the open source release is at a beta stage, and 10 beta releases of the source have been made. We anticipate a complete open source release in first quarter 2008.<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> [[Image:histo_matching.jpg]]<br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18194 2007-11-28T14:09:46Z

<p>Fischl: /* Numerical Recipies Replacement */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset.&lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:overcomplete_vs_biorthogonal_wavelets.tif|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. We propose a technique to accurately correct<br /> the spherical topology of cortical surfaces. Specifically,we construct<br /> a mapping from the original surface onto the sphere to detect<br /> topological defects as minimal nonhomeomorphic regions. The<br /> topology of each defect is then corrected by opening and sealing<br /> the surface along a set of nonseparating loops that are selected in<br /> a Bayesian framework. The proposed method is a wholly self-contained<br /> topology correction algorithm, which determines geometrically<br /> accurate, topologically correct solutions based on the magnetic<br /> resonance imaging (MRI) intensity profile and the expected<br /> local curvature. Applied to real data, our method provides topological<br /> corrections similar to those made by a trained operator.<br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:separating_loops.jpg|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. This project has been completed through the use of the open source packages VNL and Cephes. This includes the complete replacement of all Numerical Recipes in C code, and the implementation of a battery of unit tests for each replaced function. Currently the open source release is at a beta stage, and 10 beta releases of the source have been made. We anticipate a complete open source release in first quarter 2008.<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=File:Separating_loops.jpg&diff=18193 2007-11-28T14:06:31Z

<p>Fischl: Nonseparating loops on an open surface. (a) Patch with three topological defects (i.e., handles). (b) The wavefront intersection is used to identify a handle on the surface. Note that the remaining faces in the defect are connected and that two associated</p> <hr /> <div>Nonseparating loops on an open surface. (a) Patch with three topological defects (i.e., handles). (b) The wavefront intersection is used to identify a handle<br /> on the surface. Note that the remaining faces in the defect are connected and that two associated nonseparating loops are identified: choosing the “green” loop<br /> corrects the topology by cutting the handle, while choosing the “yellow” one fills the corresponding hole. The magnified region illustrates the wavefront intersection<br /> with two triangles (dashed region) intersecting in a single vertex. (c) The front intersection indicates the potential presence of a handle in the defect. In this example,<br /> the rest of the faces are connected but not within the defect: this wavefront evolution can be used to locate only one single nonseparating loop, which, in this case,<br /> corresponds to filling the hole. We note that other wavefront evolutions (i.e., starting from other seed faces) will often produce two nonseparating loops, and not<br /> always one single nonseparating loop. (d) A wavefront intersection does not always imply that a nonseparating loop exists, as this example illustrates: the remaining<br /> faces are not connected. Therefore, we continue evolving the front.</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18192 2007-11-28T14:05:49Z

<p>Fischl: /* Topology Correction */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset.&lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:overcomplete_vs_biorthogonal_wavelets.tif|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. We propose a technique to accurately correct<br /> the spherical topology of cortical surfaces. Specifically,we construct<br /> a mapping from the original surface onto the sphere to detect<br /> topological defects as minimal nonhomeomorphic regions. The<br /> topology of each defect is then corrected by opening and sealing<br /> the surface along a set of nonseparating loops that are selected in<br /> a Bayesian framework. The proposed method is a wholly self-contained<br /> topology correction algorithm, which determines geometrically<br /> accurate, topologically correct solutions based on the magnetic<br /> resonance imaging (MRI) intensity profile and the expected<br /> local curvature. Applied to real data, our method provides topological<br /> corrections similar to those made by a trained operator.<br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:separating_loops.jpg|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18191 2007-11-28T14:02:44Z

<p>Fischl: /* Tensor-based group comparison (Cramer test) */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset.&lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:overcomplete_vs_biorthogonal_wavelets.tif|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18190 2007-11-28T14:02:30Z

<p>Fischl: /* QBall Visualization */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset.&lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:overcomplete_vs_biorthogonal_wavelets.tif|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> == [[Algorithm:MGH:Development:GroupComp|Tensor-based group comparison (Cramer test)]] ==<br /> <br /> Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Paper submitted: &quot;Statistical Group Comparison of Diffusion Tensors via Multivariate Hypothesis Testing.&quot;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=File:Overcomplete_vs_biorthogonal_wavelets.tif&diff=18189 2007-11-28T14:01:17Z

<p>Fischl: Comparison of overcomplete and biorthogonal wavelets</p> <hr /> <div>Comparison of overcomplete and biorthogonal wavelets</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18188 2007-11-28T14:00:49Z

<p>Fischl: /* Spherical Wavelets */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset.&lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:overcomplete_vs_biorthogonal_wavelets.tif|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:QBALLVisualization|QBall Visualization]] ==<br /> <br /> Our objective is to visualize q-ball data in Slicer. [[Algorithm:MGH:QBALLVisualization|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:GroupComp|Tensor-based group comparison (Cramer test)]] ==<br /> <br /> Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Paper submitted: &quot;Statistical Group Comparison of Diffusion Tensors via Multivariate Hypothesis Testing.&quot;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=File:Placeholder.png&diff=18187 2007-11-28T13:59:02Z

<p>Fischl: Comparison of overcomplete and biorthogonal wavelet bases</p> <hr /> <div>Comparison of overcomplete and biorthogonal wavelet bases</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18186 2007-11-28T13:55:10Z

<p>Fischl: /* Spherical Wavelets */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset.&lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | |<br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:QBALLVisualization|QBall Visualization]] ==<br /> <br /> Our objective is to visualize q-ball data in Slicer. [[Algorithm:MGH:QBALLVisualization|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:GroupComp|Tensor-based group comparison (Cramer test)]] ==<br /> <br /> Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Paper submitted: &quot;Statistical Group Comparison of Diffusion Tensors via Multivariate Hypothesis Testing.&quot;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18185 2007-11-28T13:53:53Z

<p>Fischl: /* Adding NRRD I/O to Freesurfer */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. This project allows the seemless exchange of diffusion-based volumetric data between Slicer and the FreeSurfer analysis stream, including tensors, eigendirections, as well as raw muli-direction diffusion data.<br /> [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. [[Algorithm:MGH:Development:SphericalWavelets|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:QBALLVisualization|QBall Visualization]] ==<br /> <br /> Our objective is to visualize q-ball data in Slicer. [[Algorithm:MGH:QBALLVisualization|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:GroupComp|Tensor-based group comparison (Cramer test)]] ==<br /> <br /> Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Paper submitted: &quot;Statistical Group Comparison of Diffusion Tensors via Multivariate Hypothesis Testing.&quot;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18183 2007-11-28T13:52:03Z

<p>Fischl: /* Engineering:Project:Non-rigid_EPI_registration */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. [[Algorithm:MGH:Development:SphericalWavelets|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:QBALLVisualization|QBall Visualization]] ==<br /> <br /> Our objective is to visualize q-ball data in Slicer. [[Algorithm:MGH:QBALLVisualization|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:GroupComp|Tensor-based group comparison (Cramer test)]] ==<br /> <br /> Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Paper submitted: &quot;Statistical Group Comparison of Diffusion Tensors via Multivariate Hypothesis Testing.&quot;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=18182 2007-11-28T13:51:51Z

<p>Fischl: /* Optimal path calculator (Poistats) */</p> <hr /> <div>Back to [[Algorithm:Main|NA-MIC Algorithms]]<br /> <br /> = Overview of MGH Algorithms =<br /> <br /> A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).<br /> <br /> = MGH Projects =<br /> <br /> {|<br /> | style=&quot;width:10%&quot; | [[Image:placeholder.png|left|200px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> == [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==<br /> <br /> Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> <br /> <br /> == [[Engineering:Project:Non-rigid_EPI_registration|Engineering:Project:Non-rigid_EPI_registration]] ==<br /> <br /> My objective is to evaluate the benefit of using ITK nonlinear registration for group FA comparisons. [[Engineering:Project:Non-rigid_EPI_registration|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==<br /> <br /> Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. [[Algorithm:MGH:NRDDFreesurfer|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==<br /> Cortical Surface Shape Analysis Based on Spherical Wavelets. [[Algorithm:MGH:Development:SphericalWavelets|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==<br /> Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007<br /> <br /> &lt;br /&gt;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:QBALLVisualization|QBall Visualization]] ==<br /> <br /> Our objective is to visualize q-ball data in Slicer. [[Algorithm:MGH:QBALLVisualization|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Put something new here.<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:GroupComp|Tensor-based group comparison (Cramer test)]] ==<br /> <br /> Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Paper submitted: &quot;Statistical Group Comparison of Diffusion Tensors via Multivariate Hypothesis Testing.&quot;<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==<br /> <br /> Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; Completed<br /> <br /> |-<br /> <br /> | | [[Image:placeholder.png|thumb|left|200px]]<br /> | | <br /> <br /> == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==<br /> <br /> Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]<br /> <br /> &lt;font color=&quot;red&quot;&gt;'''New: '''&lt;/font&gt; IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007</div>

Fischl https://www.na-mic.org/w/index.php?title=2007_Core_1_Meeting&diff=10969 2007-05-30T12:48:37Z

<p>Fischl: /* Attendees */</p> <hr /> <div>== Agenda ==<br /> <br /> *May 30 - <br /> ** 8:30am Remarks (Whitaker)<br /> *** Introductions<br /> *** Discuss goals and agenda<br /> ** 9:00am Driving Biological problems '''[[2007_Core_1_Meeting_DBP_Guidlines|(Guidelines for talks)]]'''<br /> *** Marek Kubicki - Harvard/B&amp;W<br /> *** Gabor Fichtinger - Johns Hopkins<br /> *** (break)<br /> *** H. Jeremy Bockholt - Mind Institute<br /> *** Heather Cody Hazlett - UNC<br /> **11:30pm Core 1 Coordinate Discussion<br /> *** A preliminary discussion in preparation for agenda items on Thurs afternoon. For example --- software dissemination.<br /> **12:00pm Lunch<br /> ** 1:00pm Invited Talk: Daniel Rueckert. &quot;Quantification of brain development during early childhood using non-rigid registration&quot;. ([http://www.csail.mit.edu/events/eventcalendar/calendar.php?show=event&amp;id=1484 talk announcement])<br /> ** 2:00pm Break out sessions with DPBs<br /> ** 3:30pm Break<br /> ** 3:45-6:00pm Core 1 presentations<br /> *** John Melonakos (Georgia Tech) - TBD<br /> *** Bruce Fischl (MGH) &quot;Predicting architectonic boundaries from folding patterns&quot;<br /> *** Serdar Balci (MIT), &quot;Group-wise registration in NAMIC-kit&quot;<br /> *** Guido Gerig (UNC), &quot;DTI atlas building with application to PNL SZ study (C. Goodlett)&quot; <br /> *** Tom Fletcher (Utah), &quot;Volumetric Connectivity for analysis of DTI&quot;<br /> *May 31<br /> ** 8:30am Core 1 presentations<br /> *** Utah &quot;Nonparametric Shape Modeling of Object Complexes&quot; (Speaker TBD)<br /> *** Guido Gerig (UNC) &quot;UNC Shape Analysis (M. Styner, I. Oguz)&quot; / &quot;Constructing Image Graphs for Lesion Segmention (M. Prastawa)&quot;<br /> *** (break)<br /> *** Mert Sabuncu (MIT), &quot;Population Analysis of Anatomical Variability&quot; <br /> *** Gheorghe Postelnicu (MGH), &quot;5D warping: integrating volume and surface information&quot;<br /> *** John Melonakos (Georgia Tech) - TBD<br /> ** 12:30pm Lunch<br /> ** 1pm Strategic planning, software<br /> *** Progress/interactions with DBPs<br /> *** Software contributions and Core 2 interactions<br /> *** Performance assessment and renewal<br /> ** 5pm Finish<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' May 30-31, 2007. <br /> <br /> Please plan to travel on May 29, so that we can start in the morning of May 30.<br /> The meeting will be two full days; please plan to stay until 5pm on May31.<br /> <br /> '''Location:''' MIT.<br /> <br /> The meeting will take place in the Kiva conference room, on the 4th floor of Stata Center. We will post signs in the building, directing you to the conference room.<br /> <br /> '''Food:''' Breakfast and lunch will be provided on May 30-31. We will also organize people into groups to go out for dinner on May 30. There are plenty of restaurants around Central Square and MIT.<br /> <br /> '''Hotel:''' There is no official hotel for the meeting. Here is some information about Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Please book your rooms early.<br /> <br /> <br /> == Attendees ==<br /> <br /> #Ross Whitaker (Utah)<br /> #Polina Golland (MIT)<br /> #Ron Kikinis (BWH)<br /> #Guido Gerig(UNC)<br /> #Heather Cody Hazlett (UNC Autism DBP)<br /> #Allen Tannenbaum (Georgia Tech)<br /> #John Melonakos (Georgia Tech)<br /> #H. Jeremy Bockholt (MIND/UNM)<br /> #Harvard Core 3: Marek Kubicki<br /> #Mert R Sabuncu (MIT CSAIL)<br /> #Lilla Zollei (NMR, MGH)<br /> #Serdar K Balci (MIT CSAIL)<br /> #Ulas Ziyan (MIT)<br /> #Tom Fletcher (Utah)<br /> #Josh Cates (Utah - tentative)<br /> #Gabor Fichtinger (JHU)<br /> #Jim Miller (GE Research)<br /> #Dennis Jen (MGH)<br /> #Sandy Wells (BWH, MIT)<br /> #Marc Niethammer (BWH, Core 3)<br /> #Wanmei Ou (MIT)<br /> # Purang Abolmaesumi (Queen's)<br /> # Steve Pieper (Isomics, Core 2)<br /> # Peng Yu (HST/MIT)<br /> # Gheorghe Postelnicu (MGH)<br /> # Bruce Fischl (MGH)</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=8853 2007-04-03T21:02:30Z

<p>Fischl: /* In Development */</p> <hr /> <div>== Coordination ==<br /> <br /> [[Algorithm:MGH:Coordination:Meeting_2004-11-17|2004-11-17 meeting @ MGH]]<br /> <br /> [[Algorithm:MGH:Coordination:Meeting_2005-1-21|2005-1-21 meeting @ BWH]]<br /> <br /> == Projects ==<br /> <br /> === In Development ===<br /> <br /> '''QDEC: An easy to use GUI for group morphometry studies'''<br /> * Difficulty: Medium<br /> * Impact: High<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Compare the primary eigendirection in two groups to see if they are the same' &lt;/nowiki&gt;<br /> * Difficulty: Low<br /> * Impact: Medium<br /> <br /> '''Optimal path calculator (Poistats)'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Specify 2 points in a diffusion image and tell how connected they are.' &lt;/nowiki&gt;<br /> * Difficulty: High<br /> * Impact: High<br /> <br /> See [[AHM_2006:ProjectsDTIPathOfInterest|AHM 2006:ProjectsDTIPathOfInterest]]<br /> <br /> &lt;br /&gt;'''Statistical power benefit of ITK nonlinear registration'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Evaluate benefit of using ITK nonlinear registration for group FA comparisons' &lt;/nowiki&gt;<br /> * Difficulty: Low-Medium<br /> * Impact: Medium<br /> <br /> See: [[Engineering:Project:Non-rigid_EPI_registration|Engineering:Project:Non-rigid_EPI_registration]]<br /> <br /> &lt;br /&gt;'''Adding NRRD I/O to Freesurfer'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Open a NRRD volume in FreeSurfer.' &lt;/nowiki&gt;<br /> * '''Use case'''&lt;nowiki&gt;: 'Convert an MGH volume to a NRRD volume with Freesurfer.' &lt;/nowiki&gt;<br /> * Difficulty: Low<br /> * Impact: Medium<br /> <br /> # Write unit tests for new IO functions (Snyder): '''in progress'''<br /> # Add NrrdIO libraries from Teem to FS source tree, build with autoconf (Snyder): '''done'''<br /> # Write and test FS NRRD IO functions (Snyder, Kindlmann): '''in progress'''<br /> # Develop approriate headers for MGH DWI data (Teich): '''queued'''<br /> # Automate header generation when possible (Teich): '''queued'''<br /> <br /> &lt;br /&gt;'''Cortical Surface Shape Analysis Based on Spherical Wavelets'''<br /> <br /> &lt;br /&gt;'''Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops'''<br /> <br /> &lt;br /&gt;<br /> <br /> * '''queued''' - step identified/specd<br /> * '''in progress''' - step in progress<br /> * '''done''' - step complete<br /> <br /> === Done ===<br /> <br /> '''QBALL visualization'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Visualize q-ball data in Slicer.' &lt;/nowiki&gt;<br /> * Difficulty: Low<br /> * Impact: Medium<br /> <br /> # Implement ODF polygon decimation algorithm (Tuch) : '''done'''<br /> # Port decimation fileformat into FreeDiffusion Visualizer (Snyder) : '''done'''<br /> # Port QBALL/ODF visualization into [[Slicer|Slicer]] (Estepar/Snyder/Kindlmann/Tuch/Westin): '''done'''<br /> ## Implement (Estepar): '''done'''<br /> ## Test on mock data set (Estepar): '''done'''<br /> ## Demo for real data set (Estepar/Snyder/Kindlmann): '''done'''<br /> <br /> '''Tensor-based group comparison (Cramer test)'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Compare DTI images between groups using the full tensor information.' &lt;/nowiki&gt;<br /> * Difficulty: Medium<br /> * Impact: Medium-High<br /> <br /> # Implement in R (Whitcher/Tuch) : '''done'''<br /> # Power analysis (Whitcher) : '''done'''<br /> # Port to Matlab (Whitcher) : '''done'''<br /> # Validate Matlab version against R (Whitcher) : '''done'''<br /> # Test on group data : '''done'''<br /> # Release bootstrap-only version to test group: '''done'''<br /> # Port FFT method from R to matlab (Whitcher): '''done'''<br /> # Implement FFT method in diffusion development environment (Tuch): '''done'''<br /> <br /> See [[Algorithm:MGH:Development:GroupComp|Algorithm:MGH:Development:GroupComp]]<br /> <br /> &lt;br /&gt;'''Replacing Numerical Recipes in FreeSurfer (for open sourcing)'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Unit tests pass with all replacements.' &lt;/nowiki&gt;<br /> * Difficulty: Medium-High<br /> * Impact: High<br /> <br /> # Write test cases for each algorithm (Snyder, Jen): '''done'''<br /> # Identify replacements (Snyder, Jen): '''done'''<br /> # Integrate required libraries into FreeSurfer build process (Snyder, Jen): '''done'''<br /> # Iteratively replace recipes with substitutes and run tests (Snyder, Jen): '''done'''<br /> <br /> &lt;br /&gt;'''Intensity Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms'''<br /> <br /> * '''Use Case'''&lt;nowiki&gt;: 'Atlas-based fully automated whole brain segmentation' &lt;/nowiki&gt;<br /> * Difficulty: Medium-High<br /> * Impact: Medium-High<br /> <br /> # Implemented in C and distribute with the FreeSurface Package: '''done'''</div>

Fischl https://www.na-mic.org/w/index.php?title=Algorithm:MGH&diff=8852 2007-04-03T21:01:13Z

<p>Fischl: /* In Development */</p> <hr /> <div>== Coordination ==<br /> <br /> [[Algorithm:MGH:Coordination:Meeting_2004-11-17|2004-11-17 meeting @ MGH]]<br /> <br /> [[Algorithm:MGH:Coordination:Meeting_2005-1-21|2005-1-21 meeting @ BWH]]<br /> <br /> == Projects ==<br /> <br /> === In Development ===<br /> <br /> '''Primary Eigenvector Group Statistics Using Matrix Log Transform'''<br /> * '''Use case'''&lt;nowiki&gt;: 'Compare the primary eigendirection in two groups to see if they are the same' &lt;/nowiki&gt;<br /> * Difficulty: Low<br /> * Impact: Medium<br /> <br /> '''Optimal path calculator (Poistats)'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Specify 2 points in a diffusion image and tell how connected they are.' &lt;/nowiki&gt;<br /> * Difficulty: High<br /> * Impact: High<br /> <br /> See [[AHM_2006:ProjectsDTIPathOfInterest|AHM 2006:ProjectsDTIPathOfInterest]]<br /> <br /> &lt;br /&gt;'''Statistical power benefit of ITK nonlinear registration'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Evaluate benefit of using ITK nonlinear registration for group FA comparisons' &lt;/nowiki&gt;<br /> * Difficulty: Low-Medium<br /> * Impact: Medium<br /> <br /> See: [[Engineering:Project:Non-rigid_EPI_registration|Engineering:Project:Non-rigid_EPI_registration]]<br /> <br /> &lt;br /&gt;'''Adding NRRD I/O to Freesurfer'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Open a NRRD volume in FreeSurfer.' &lt;/nowiki&gt;<br /> * '''Use case'''&lt;nowiki&gt;: 'Convert an MGH volume to a NRRD volume with Freesurfer.' &lt;/nowiki&gt;<br /> * Difficulty: Low<br /> * Impact: Medium<br /> <br /> # Write unit tests for new IO functions (Snyder): '''in progress'''<br /> # Add NrrdIO libraries from Teem to FS source tree, build with autoconf (Snyder): '''done'''<br /> # Write and test FS NRRD IO functions (Snyder, Kindlmann): '''in progress'''<br /> # Develop approriate headers for MGH DWI data (Teich): '''queued'''<br /> # Automate header generation when possible (Teich): '''queued'''<br /> <br /> &lt;br /&gt;'''Cortical Surface Shape Analysis Based on Spherical Wavelets'''<br /> <br /> &lt;br /&gt;'''Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops'''<br /> <br /> &lt;br /&gt;<br /> <br /> * '''queued''' - step identified/specd<br /> * '''in progress''' - step in progress<br /> * '''done''' - step complete<br /> <br /> === Done ===<br /> <br /> '''QBALL visualization'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Visualize q-ball data in Slicer.' &lt;/nowiki&gt;<br /> * Difficulty: Low<br /> * Impact: Medium<br /> <br /> # Implement ODF polygon decimation algorithm (Tuch) : '''done'''<br /> # Port decimation fileformat into FreeDiffusion Visualizer (Snyder) : '''done'''<br /> # Port QBALL/ODF visualization into [[Slicer|Slicer]] (Estepar/Snyder/Kindlmann/Tuch/Westin): '''done'''<br /> ## Implement (Estepar): '''done'''<br /> ## Test on mock data set (Estepar): '''done'''<br /> ## Demo for real data set (Estepar/Snyder/Kindlmann): '''done'''<br /> <br /> '''Tensor-based group comparison (Cramer test)'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Compare DTI images between groups using the full tensor information.' &lt;/nowiki&gt;<br /> * Difficulty: Medium<br /> * Impact: Medium-High<br /> <br /> # Implement in R (Whitcher/Tuch) : '''done'''<br /> # Power analysis (Whitcher) : '''done'''<br /> # Port to Matlab (Whitcher) : '''done'''<br /> # Validate Matlab version against R (Whitcher) : '''done'''<br /> # Test on group data : '''done'''<br /> # Release bootstrap-only version to test group: '''done'''<br /> # Port FFT method from R to matlab (Whitcher): '''done'''<br /> # Implement FFT method in diffusion development environment (Tuch): '''done'''<br /> <br /> See [[Algorithm:MGH:Development:GroupComp|Algorithm:MGH:Development:GroupComp]]<br /> <br /> &lt;br /&gt;'''Replacing Numerical Recipes in FreeSurfer (for open sourcing)'''<br /> <br /> * '''Use case'''&lt;nowiki&gt;: 'Unit tests pass with all replacements.' &lt;/nowiki&gt;<br /> * Difficulty: Medium-High<br /> * Impact: High<br /> <br /> # Write test cases for each algorithm (Snyder, Jen): '''done'''<br /> # Identify replacements (Snyder, Jen): '''done'''<br /> # Integrate required libraries into FreeSurfer build process (Snyder, Jen): '''done'''<br /> # Iteratively replace recipes with substitutes and run tests (Snyder, Jen): '''done'''<br /> <br /> &lt;br /&gt;'''Intensity Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms'''<br /> <br /> * '''Use Case'''&lt;nowiki&gt;: 'Atlas-based fully automated whole brain segmentation' &lt;/nowiki&gt;<br /> * Difficulty: Medium-High<br /> * Impact: Medium-High<br /> <br /> # Implemented in C and distribute with the FreeSurface Package: '''done'''</div>

Fischl https://www.na-mic.org/w/index.php?title=2007_Annual_Scientific_Report&diff=8851 2007-04-03T20:50:27Z

<p>Fischl: /* Key Investigators */</p> <hr /> <div>Back to [[2007_Progress_Report]]<br /> <br /> == 1. Introduction ==<br /> <br /> <br /> <br /> == 2. Four Main Themes ==<br /> <br /> This year's activities focus on four main themes: Diffusion Image Analysis, Structural Analysis, Functional MRI Analysis, and the NA-MIC Kit. Each of the following sections begins with an overview of the theme, provides a progress update and list of key investigators, and concludes with a set of links to additional information for individual projects in that theme.<br /> <br /> These thematic activities involve scientists from each of the 7 NA-MIC cores (Appendix).<br /> <br /> * Core 1 Algorithms-Ross Whitaker PI<br /> * Core 2 Engineering-Will Schroeder PI<br /> * Core 3 DBP1-Martha Shenton PI / DBP2-Andy Saykin PI / DBP3-Steven Potkin PI<br /> * Core 4 Service-Will Schroeder PI<br /> * Core 5 Training-Randy Gollub PI<br /> * Core 6 Dissemination-Tina Kapur Co-PI; Steve Pieper Co-PI<br /> * Core 7 Leadership-Ron Kikinis<br /> <br /> === 2.1 Diffusion Image Analysis Theme (Martha Shenton, Marek Kubicki)===<br /> <br /> ==== Progress ====<br /> <br /> <br /> <br /> ==== Key Investigators ====<br /> <br /> * BWH: Martha Shenton, Marek Kubicki, Marc Niethammer, Sylvain Bouix, Mark Dreusicke, Carl-Fredrik Westin, Raul San Jose, Gordon Kindlmann, Doug Markant<br /> * Harvard/MGH: Bruce Fischl, Denis Jen, David Kennedy<br /> * MIT: Lauren O'Donnell<br /> * UCI: James Fallon, Martina Panzenboeck<br /> * UNC: Guido Gerig, Isabelle Corouge, Casey Goodlett, Martin Styner<br /> * Utah: Tom Fletcher, Ross Whitaker, Saurav Basu<br /> * Georgia Tech: Eric Pichon, John Melonakos, Xavier LeFaucheur, Allen Tannenbaum<br /> * Dartmouth: John West, Andrew Saykin, Laura Flashman, Paul Wang, Heather Pixley, Robert Roth<br /> * Isomics: Steve Pieper<br /> <br /> ==== Additional Information ====<br /> <br /> For details of each of the projects in this theme, please see [[NA-MIC_Internal_Collaborative_Projects#Diffusion_Image_Analysis|NA-MIC Projects on Diffusion Image Analysis]].<br /> <br /> === 2.2 Structural Analysis Theme (Allen Tannenbaum, Martin Styner)===<br /> <br /> ==== Progress ====<br /> <br /> <br /> <br /> ==== Key Investigators ====<br /> <br /> * MIT: Kilian Pohl, Sandy Wells, Eric Grimson<br /> * UNC: Martin Styner, Ipek Oguz, Guido Gerig<br /> * Utah: Ross Whitaker, Suyash Awate, Tolga Tasdizen, Tom Fletcher, Joshua Cates, Miriah Meyer<br /> * GaTech: Allen Tannenbaum, John Melonakos, Tauseef ur Rehman, Shawn Lankton, Ramsey Al-Hakim, Eric Pichon, Delphine Nain, Oleg Michailovich, Yogesh Rathi, James Malcolm<br /> * Steve Pieper, Bill Lorensen, Luis Ibanez, Karthik Krishnan, Michael J. Pan, Jagadeeswaran Rajendiran, Jim Miller, Karthik Krishnan, Luis Ibanez<br /> * Harvard PNL: Sylvain Bouix, Motoaki Nakamura, Min-Seong Koo, Martha Shenton, Marc Niethammer, Jim Levitt<br /> * Dartmouth: Andrew Saykin<br /> * UCI: James Fallon<br /> <br /> ==== Additional Information ====<br /> <br /> For details of each of the projects in this theme, please see [[NA-MIC_Internal_Collaborative_Projects#Structural_Image_Analysis|NA-MIC Projects on Structural Image Analysis]].<br /> <br /> === 2.3 Functional MRI Analysis Theme (Polina Golland, Andy Saykin)===<br /> <br /> This theme will not be included in the report this year because the majority of the resources in the center were used to focus on DTI and Structural Analysis.<br /> <br /> === 2.4 NA-MIC Kit Theme (Jim Miller)===<br /> <br /> ==== Progress ====<br /> <br /> <br /> <br /> ==== Key Investigators ====<br /> <br /> * GE: Bill Lorensen, Jim Miller, Xiaodong Tao, Dan Blezek<br /> * Isomics: Steve Pieper, Alex Yarmarkovich<br /> * Kitware: Will Schroeder, Luis Ibanez, Karthik Krishnan, Andy Cedilnik, Sebastien Barre, Mathieu Malaterre<br /> * UCLA: Mike Pan, Jagadeeswaran Rajendiran<br /> * UCSD: Neil Jones, Jeffrey Grethe<br /> * Harvard: Nicole Aucoin, Katie Hayes, Wendy Plesniak, Mike Halle, Gordon Kindlmann, Raul San Jose Estepar, Haiying Liu, Ron Kikinis<br /> * MIT: Lauren O'Donnell, Kilian Pohl<br /> <br /> ==== Additional Information ====<br /> <br /> For details of each of the projects in this theme, please see [[NA-MIC_Internal_Collaborative_Projects#NA-MIC_Kit|NA-MIC Kit Projects]].<br /> <br /> == 3. Highlights (Will Schroeder)==<br /> <br /> == 4. Impact and Value to Biocomputing (Will Schroeder/Jim Miller)==<br /> <br /> <br /> === 4.1 Impact within the Center ===<br /> <br /> <br /> <br /> === 4.2 Impact within NIH Funded Research ===<br /> <br /> <br /> <br /> === 4.3 National and International Impact ===<br /> <br /> == 5.NA-MIC Timeline (Ross Whitaker)==<br /> <br /> This section provides a table of NAMIC timelines from the original proposal that graphically depicts completed tasks/goals in years 1, 2, and 3 and tasks/goals to be completed in years 4-5. Changes to the original timelines have also been described.<br /> <br /> [[2007_Scientific_Report_Timeline|2007 Scientific Report Timeline]]<br /> <br /> == 6. EAB Report ==<br /> <br /> The NA-MIC External Advisory Board (EAB), chaired by Prof. Chris Johnson of the University of Utah, met at the annual All-Hands Meeting. After individual presentations by NA-MIC investigators and open as well as closed-door EAB discussion, the Board provided its independent expert assessment of the Center (Appendix 2).<br /> <br /> = Logistics =<br /> <br /> == Schedule for preparation of this report ==<br /> <br /> * March 16th - Assign section/theme leads (Ron). Last year: introduction (marty), structural analysis (allen, martin), dti (guido, marty/marek), fmri (polina, andy), namic kit(bill), timeline (ross), highlights (will), impact (bill).<br /> * April 15- complete project description pages (all project owners).<br /> * April 30 - Introduction and final review (Marty)<br /> * May 15, midnight - final version submitted to NA-MIC editor (Ann)<br /> * May 28 - final edited version given to Sanjay (Ann)<br /> <br /> == Guidelines from NIH Program Officer ==<br /> <br /> The following guidelines were provided by Grace Peng, NA-MIC program officer, in Feb 2006.<br /> <br /> The key is to synthesize all the individual elements into bigger picture stories that really speak of each area’s impact to the community.<br /> <br /> The specialized scientific report should have the following format:<br /> <br /> # Introductory page describing the new grouping of NAMIC project themes.<br /> # A description of progress in each NAMIC project theme (not to exceed 2 pages each), tying together relevant activities from participating subcomponents and referencing cores in parentheses.<br /> # A table of NAMIC timelines (from original proposal), graphically depicting completed tasks/goals in years 1,2, and 3 and tasks/goals to be completed in years 4-5. Changes to the original timelines should be described.<br /> # A description of 3 highlights selected from all NAMIC projects to showcase NAMIC.<br /> # A discussion of NAMIC’s impact and value to the biocomputing community this year.</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7350 2007-01-29T17:13:53Z

<p>Fischl: </p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata Center, Seminar Room G449 ([[Meeting_Locations:MIT_CSAIL_Star|Patil Conference Room / Kiva]])<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **11.00-11.15 Bruce Rosen, Overview<br /> **11.15-11.40 Bruce Fischl, High resolution anatomical modeling<br /> **11.40-11.55 Larry Wald, High resolution structural and functional MRI<br /> ** Graham Wiggins, Large-N arrays<br /> **David Boas, Optical Imaging<br /> **Matti Hamalainen, MEG and mulit-modal inverse problems.<br /> *12.30-01.00 pm Lunch Break<br /> <br /> ==01.00-02.30 BWH==<br /> **01.00-01.10 Ron Kikinis: [[media:2007-01-29-NAC-Intro.ppt |Overview]]<br /> **01.10-01.20 CF Westin: Diffusion MRI<br /> **01.20-01.30 Sandy Wells: fMRI Informatics<br /> **01.30-01.40 Andrea Mewes: Neonate Imaging<br /> **01.40-01.50 Florin Talos: Computational Neuroanatomy<br /> **01.50-02.00 Buffer<br /> **02.00-02.10 Michael Halle: Visualization and representation for atlases<br /> **02.10-02.20 Domink Meier: Time Series Analysis PI<br /> **02.20-02.30 Steve Pieper: Status and plans for Slicer3 [[media:Pieper-eng-retreat2007-01-29.ppt | Slides]]<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl<br /> #David Boas<br /> #Larry Wald<br /> #Matti Hamalainen<br /> #Bruce Rosen<br /> #Carl-Fredrik Westin<br /> #Juliette Selb<br /> #Lilla Zollei<br /> #Jean Augustinack<br /> #Kinh Tieu<br /> #Anna Custo<br /> #Thomas Witzel<br /> #Wanmei Ou<br /> #Florin Talos<br /> #Michael Halle<br /> #Andrea Mewes<br /> #Polina Golland<br /> #Sandy Wells</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7222 2007-01-25T21:16:22Z

<p>Fischl: /* Participants */</p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen, Overview<br /> **Bruce Fischl, High resolution anatomical modeling<br /> **David Boas, Optical Imaging<br /> **Larry Wald, High resolution structural and functional MRI<br /> **Matti Hamalainen, MEG and mulit-modal inverse problems.<br /> *12.30-01.00 pm Break<br /> <br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin, Diffusion MRI<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> **Florin Talos<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl<br /> #David Boas<br /> #Larry Wald<br /> #Matti Hamalainen<br /> #Bruce Rosen<br /> #Carl-Fredrik Westin<br /> #Juliette Selb<br /> #Lilla Zollei<br /> #Jean Augustinack<br /> #Kinh Tieu<br /> #Anna Custo<br /> #Thomas Witzel<br /> #Wanmei Ou</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7218 2007-01-25T21:09:36Z

<p>Fischl: /* Participants */</p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen, Overview<br /> **Bruce Fischl, High resolution anatomical modeling<br /> **David Boas, Optical Imaging<br /> **Larry Wald, High resolution structural and functional MRI<br /> **Matti Hamalainen, MEG and mulit-modal inverse problems.<br /> *12.30-01.00 pm Break<br /> <br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin, Diffusion MRI<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> **Florin Talos<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl<br /> #David Boas<br /> #Larry Wald<br /> #Matti Hamalainen<br /> #Bruce Rosen<br /> #Carl-Fredrik Westin<br /> #Juliette Selb<br /> #Lilla Zollei<br /> #Jean Augustinack<br /> #Kinh Tieu<br /> #Anna Custo<br /> #Thomas Witzel</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7214 2007-01-25T21:02:02Z

<p>Fischl: /* Participants */</p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen, Overview<br /> **Bruce Fischl, High resolution anatomical modeling<br /> **David Boas, Optical Imaging<br /> **Larry Wald, High resolution structural and functional MRI<br /> **Matti Hamalainen, MEG and mulit-modal inverse problems.<br /> *12.30-01.00 pm Break<br /> <br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin, Diffusion MRI<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> **Florin Talos<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl<br /> #David Boas<br /> #Larry Wald<br /> #Matti Hamalainen<br /> #Bruce Rosen<br /> #Carl-Fredrik Westin<br /> #Juliette Selb<br /> #Lilla Zollei<br /> #Jean Augustinack<br /> #Kinh Tieu<br /> #Anna Custo</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7199 2007-01-25T15:24:28Z

<p>Fischl: /* 11.00-12.30 MGH */</p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen, Overview<br /> **Bruce Fischl, High resolution anatomical modeling<br /> **David Boas, Optical Imaging<br /> **Larry Wald, High resolution structural and functional MRI<br /> **Matti Hamalainen, MEG and mulit-modal inverse problems.<br /> *12.30-01.00 pm Break<br /> <br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin, Diffusion MRI<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> **Florin Talos<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl<br /> #David Boas<br /> #Larry Wald<br /> #Matti Hamalainen<br /> #Bruce Rosen<br /> #Carl-Fredrik Westin<br /> #Juliette Selb<br /> #Lilla Zollei<br /> #Jean Augustinack</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7198 2007-01-25T15:23:19Z

<p>Fischl: /* 11.00-12.30 MGH */</p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen<br /> **Bruce Fischl<br /> **David Boas<br /> **Larry Wald<br /> **Matti Hamalainen<br /> *12.30-01.00 pm Break<br /> <br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin, Diffusion MRI<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> **Florin Talos<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl<br /> #David Boas<br /> #Larry Wald<br /> #Matti Hamalainen<br /> #Bruce Rosen<br /> #Carl-Fredrik Westin<br /> #Juliette Selb<br /> #Lilla Zollei<br /> #Jean Augustinack</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7197 2007-01-25T15:22:54Z

<p>Fischl: /* Participants */</p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen<br /> **Bruce Fischl<br /> **David Boas<br /> **Larry Wald<br /> **Matti Hamalainen<br /> **Lilla Zollei<br /> *12.30-01.00 pm Break<br /> <br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin, Diffusion MRI<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> **Florin Talos<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl<br /> #David Boas<br /> #Larry Wald<br /> #Matti Hamalainen<br /> #Bruce Rosen<br /> #Carl-Fredrik Westin<br /> #Juliette Selb<br /> #Lilla Zollei<br /> #Jean Augustinack</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7196 2007-01-25T15:22:42Z

<p>Fischl: /* Participants */</p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen<br /> **Bruce Fischl<br /> **David Boas<br /> **Larry Wald<br /> **Matti Hamalainen<br /> **Lilla Zollei<br /> *12.30-01.00 pm Break<br /> <br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin, Diffusion MRI<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> **Florin Talos<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl<br /> #David Boas<br /> #Larry Wald<br /> #Matti Hamalainen<br /> #Bruce Rosen<br /> #Carl-Fredrik Westin<br /> #Juliette Selb<br /> #Lilla Zollei</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7138 2007-01-23T19:41:55Z

<p>Fischl: </p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen<br /> **Bruce Fischl<br /> **David Boas<br /> **Larry Wald<br /> **Matti Hamalainen<br /> *12.30-01.00 pm Break<br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl<br /> #David Boas<br /> #Larry Wald<br /> #Matti Hamalainen<br /> #Bruce Rosen</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7137 2007-01-23T19:41:27Z

<p>Fischl: </p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen<br /> **Bruce Fischl<br /> **David Boas<br /> **Larry Wald<br /> **Matti Hamalainen<br /> *12.30-01.00 pm Break<br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7116 2007-01-22T20:59:47Z

<p>Fischl: </p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen<br /> **Bruce Fischl<br /> *12.30-01.00 pm Break<br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> #Bruce Fischl</div>

Fischl https://www.na-mic.org/w/index.php?title=P41-2007-Joint-Retreat&diff=7115 2007-01-22T20:59:30Z

<p>Fischl: </p> <hr /> <div>=Joint Retreat =<br /> * What is the objective<br /> **To familiarize the others with the ongoing activties in the respective cores<br /> **To identify opportunities for leverage and augmentation<br /> * Who: <br /> **The MGH Center for Functional Imaging Technologies <br /> **The BWH Neuroimage Analysis Center<br /> **Core PI's for the two centers plus not more than 2 people per core<br /> * Where:<br /> **MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)<br /> * When:<br /> **Monday, Jan. 29, 11am-5pm<br /> <br /> =Agenda=<br /> ==11.00-12.30 MGH==<br /> **Bruce Rosen<br /> **Bruce Fischl<br /> *12.30-01.00 pm Break<br /> ==01.10-02.30 BWH==<br /> **Ron Kikinis<br /> **Sandy Wells<br /> **CF Westin<br /> **Andrea Mewes<br /> **Mike Halle<br /> **Domink Meier<br /> **Steve Pieper<br /> <br /> ==02.30-03.00 Break==<br /> *03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)<br /> *04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)<br /> <br /> =Participants=<br /> #Ron Kikinis, PI, NAC<br /> #Steve Pieper<br /> *Bruce Fischl</div>

Fischl https://www.na-mic.org/w/index.php?title=EAB_Meeting_AHM2007&diff=5843 2007-01-07T02:10:55Z

<p>Fischl: </p> <hr /> <div> Back to [[AHM_2007]]<br /> <br /> Information about NA-MIC EAB is available [[EAB|here]].<br /> <br /> *Confirmed EAB Attendees:<br /> **Chris Johnson (Chair)<br /> **Sanjoy Mitter<br /> **Sandy Napel<br /> **Godfrey Pearlson<br /> **Carlo Pierpaoli<br /> **Fred Prior<br /> **Michael Ackerman (ex officio)<br /> <br /> Schedule for the EAB Meeting at AHM 2007:<br /> <br /> * 8-10am: <br /> ** 5-min each Site PI Presentations to the EAB: <br /> ** What did you do for NA-MIC and/or what did NA-MIC do for you<br /> ** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation<br /> *** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf|slides]])<br /> *** Core 2: GE GRC ([[slides]]), Kitware ([[slides]]), UCLA ([[slides]]), UCSD ([[slides]]), Isomics ([[slides]])<br /> *** Core 3: Harvard ([[Media:NA-MIC_EAB_01_08_shenton_2007.ppt|slides]]), Dartmouth ([[slides]]), UCI and U Toronto ([[slides]])<br /> *** Cores 4-6: Service ([[slides]]), Dissemination ([[slides]]), Training ([[slides]])<br /> * 10-10:30am: Coffee break<br /> * 10:30am-11am: Discussion of Site PIs with EAB<br /> * 11am-12pm: Closed session of the EAB<br /> * 12pm adjourn<br /> <br /> <br /> Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]</div>

Fischl https://www.na-mic.org/w/index.php?title=EAB_Meeting_AHM2007&diff=5842 2007-01-07T02:10:10Z

<p>Fischl: </p> <hr /> <div> Back to [[AHM_2007]]<br /> <br /> Information about NA-MIC EAB is available [[EAB|here]].<br /> <br /> *Confirmed EAB Attendees:<br /> **Chris Johnson (Chair)<br /> **Sanjoy Mitter<br /> **Sandy Napel<br /> **Godfrey Pearlson<br /> **Carlo Pierpaoli<br /> **Fred Prior<br /> **Michael Ackerman (ex officio)<br /> <br /> Schedule for the EAB Meeting at AHM 2007:<br /> <br /> * 8-10am: <br /> ** 5-min each Site PI Presentations to the EAB: <br /> ** What did you do for NA-MIC and/or what did NA-MIC do for you<br /> ** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation<br /> *** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf[slides]])<br /> *** Core 2: GE GRC ([[slides]]), Kitware ([[slides]]), UCLA ([[slides]]), UCSD ([[slides]]), Isomics ([[slides]])<br /> *** Core 3: Harvard ([[Media:NA-MIC_EAB_01_08_shenton_2007.ppt|slides]]), Dartmouth ([[slides]]), UCI and U Toronto ([[slides]])<br /> *** Cores 4-6: Service ([[slides]]), Dissemination ([[slides]]), Training ([[slides]])<br /> * 10-10:30am: Coffee break<br /> * 10:30am-11am: Discussion of Site PIs with EAB<br /> * 11am-12pm: Closed session of the EAB<br /> * 12pm adjourn<br /> <br /> <br /> Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]</div>

Fischl https://www.na-mic.org/w/index.php?title=EAB_Meeting_AHM2007&diff=5841 2007-01-07T02:09:42Z

<p>Fischl: </p> <hr /> <div> Back to [[AHM_2007]]<br /> <br /> Information about NA-MIC EAB is available [[EAB|here]].<br /> <br /> *Confirmed EAB Attendees:<br /> **Chris Johnson (Chair)<br /> **Sanjoy Mitter<br /> **Sandy Napel<br /> **Godfrey Pearlson<br /> **Carlo Pierpaoli<br /> **Fred Prior<br /> **Michael Ackerman (ex officio)<br /> <br /> Schedule for the EAB Meeting at AHM 2007:<br /> <br /> * 8-10am: <br /> ** 5-min each Site PI Presentations to the EAB: <br /> ** What did you do for NA-MIC and/or what did NA-MIC do for you<br /> ** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation<br /> *** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf][slides]])<br /> *** Core 2: GE GRC ([[slides]]), Kitware ([[slides]]), UCLA ([[slides]]), UCSD ([[slides]]), Isomics ([[slides]])<br /> *** Core 3: Harvard ([[Media:NA-MIC_EAB_01_08_shenton_2007.ppt|slides]]), Dartmouth ([[slides]]), UCI and U Toronto ([[slides]])<br /> *** Cores 4-6: Service ([[slides]]), Dissemination ([[slides]]), Training ([[slides]])<br /> * 10-10:30am: Coffee break<br /> * 10:30am-11am: Discussion of Site PIs with EAB<br /> * 11am-12pm: Closed session of the EAB<br /> * 12pm adjourn<br /> <br /> <br /> Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]</div>

Fischl https://www.na-mic.org/w/index.php?title=EAB_Meeting_AHM2007&diff=5840 2007-01-07T02:07:40Z

<p>Fischl: </p> <hr /> <div> Back to [[AHM_2007]]<br /> <br /> Information about NA-MIC EAB is available [[EAB|here]].<br /> <br /> *Confirmed EAB Attendees:<br /> **Chris Johnson (Chair)<br /> **Sanjoy Mitter<br /> **Sandy Napel<br /> **Godfrey Pearlson<br /> **Carlo Pierpaoli<br /> **Fred Prior<br /> **Michael Ackerman (ex officio)<br /> <br /> Schedule for the EAB Meeting at AHM 2007:<br /> <br /> * 8-10am: <br /> ** 5-min each Site PI Presentations to the EAB: <br /> ** What did you do for NA-MIC and/or what did NA-MIC do for you<br /> ** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation<br /> *** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf]])<br /> *** Core 2: GE GRC ([[slides]]), Kitware ([[slides]]), UCLA ([[slides]]), UCSD ([[slides]]), Isomics ([[slides]])<br /> *** Core 3: Harvard ([[Media:NA-MIC_EAB_01_08_shenton_2007.ppt|slides]]), Dartmouth ([[slides]]), UCI and U Toronto ([[slides]])<br /> *** Cores 4-6: Service ([[slides]]), Dissemination ([[slides]]), Training ([[slides]])<br /> * 10-10:30am: Coffee break<br /> * 10:30am-11am: Discussion of Site PIs with EAB<br /> * 11am-12pm: Closed session of the EAB<br /> * 12pm adjourn<br /> <br /> <br /> Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]</div>

Fischl https://www.na-mic.org/w/index.php?title=File:NAMIC_MGH_AHM_2007.pdf&diff=5839 2007-01-07T02:06:06Z

<p>Fischl: </p> <hr /> <div></div>

Fischl