Difference between revisions of "Mbirn: Updates"

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'''Feb 24, 2005''' (J. Sacks)
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'''4/13/2005'''<br /> Teleconference regarding Ontology development: Behavioral Domain improvements. Angie Laird and Jessica Turner present.
  
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<br />'''Revised summary:'''
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Action Items:
  
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* As part of the fBIRN a new tool for multi-volume preview and processing , called Ibrowser , is being developed for 3D Slicer by Wendy Plesniak. A key feature of Ibrowser will be the ability to load a multi-volume set as a time series. Such time series can then be analyzed using various tools. The Ibrowser can currently load and display multi-volume sequences of images in several data formats in Slicer. Ibrowser will be extended to load perfusion sequences, enable their processing through its GUI and permit animated preview and saving. Early work on these features is already underway. Once a sequence has been motion corrected by registration, other existing Slicer tools for defining regions or volumes of interest and for performing various measurements and computations on volumes can be applied to the data. We may discover that additional specialized measurement tools may also be required to do the necessary Investigation analysis.
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1) Beginning with Attention and Working Memory as the areas to flesh out in the Behavioral domains: Ask the experts (A. Belger responded re: attention already), and check the textbooks (Jess). With an updated taxonomy (Angie), Angie can pull out papers previously stored as "Attention" and improve their descriptions (this is a long-term goal, not by April 29). This serves as another method of validation.
  
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* A critical step for being able to perform the myocardial blood perfusion analyses is firstly to co-register the set of volumes in the time series. Being able to do this quickly and accurately is a non-trivial task. The immediate goal for the group working on this project is to decide on the best method for performing the co-registration, and then to implement it within the Ibrowser module.
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Note that dividing Attention into "voluntary" and "involuntary" allows the distinction between the FBIRN Phase I MMN and the FBIRN Phase II Oddball to be represented in this dimension.
  
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# Gunner Farneback, under the guidance of C.F. Westin, has been working on a non-rigid registration algorithm which is being tested. Presumably it could be used standalone. The algorithm uses both the ITK and MATLAB packages. It does give good results compared with the current method. However, since it is tied to MATLAB, it cannot be incorporated in 3D Slicer’s Ibrowser , which will be using only ITK.
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2) Jess will do a search of UMLS on attention and working memory to get a handle on how those concepts are represented (or not). She is also in contact with the Ontology Task Force regarding the relationship between the BIRN HID and the Mediator and how the ontologies are accessed; this will affect how the taxonomy being developed here is used to best advantage.
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# Steve Pieper and Wendy Plesniak have proposed that as an initial step, a rigid co-registration be performed manually in Ibrowser on key frames to be interpolated across intermediate frames. Work on this is starting up.
 
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# In the long term it will be necessary to develop new co-registration tools for multi-volume time series in Ibrowser. It is hoped that techniques being successfully used in neuroscience registration will be transferable and will produce far greater accuracy, possibly down to the the voxel level
 
  
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<br />'''Start Date'''<nowiki>: January, 2005 </nowiki><br />'''Completion Date'''<nowiki>: no later than December,2005 </nowiki><br /><br /> The criteria for success of this project are the completion of the following: <br />'''Deliverables'''<nowiki>: </nowiki>
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3) Take an FBIRN Phase I analysis done in SPM (e.g., the MMN data for the two subjects at UCI) and represent the final results of one contrast in the BrainMap Submit method (Jess, then Angie). The current description was a quick toy based on an abstract notion of the experiment and not driven by an actual table of MNI-space maximal clusters.
  
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* (1) Comparison of available registration methods (method currently used by Adler/Kwong, Gunnar Farneback’s method, Pieper-Plesniak proposal).<br />''Status''<nowiki>: currently in process Expected completion date: March 31, 2004 </nowiki>
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3) David and Angela will review the XML/ENT modifications from 4/6/2005.
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* (2) Longer term development of multi-volume registration methods to be used in Ibrowser<br />'' Status''<nowiki>: initial work on Ibrowser has been completed by Wendy Posniak </nowiki>
 
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* (3) Incorporation or development of tools in Slicer for the quantitative analysis of myocardial blood perfusion.
 
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* (4)Application to the BWH/GCRC myocardial blood perfusion study (may begin after (1) is completed)
 
  
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<br />'''Milestones''' for GCRC meeting in April:
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4) Next call Wed April 20 at 8:30 am PDT.
  
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* (a) Results of investigation into which registration methods should to be used in Ibrowser
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<br />'''4/6/2005'''<br />
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* (b) A more refined definition of the project
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* (c) A revised workplan
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David sent the XML schema description we agreed on; Angela augmented the project-level descriptions to fit the BrainMap descriptive schema.
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'''3/22/2005'''<br /> Meeting at the FBIRN AHM regarding ontologies and BrainMap interactions. See [[Experimental_Taxonomy_Discussion|Experimental_Taxonomy_Discussion]]
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<br />'''3/17 and 3/18/2005'''<br /> Meeting at UCI between FBIRN and the San Antonio BrainMap representatives. Attendants: Jessica Turner, David Keator, Angie Laird, Angela Uecker. See [[FBIRN:BrainMap_Discussion|FBIRN:BrainMap Discussion]].
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<br />'''3/7/2005'''<br /> Ontology Task Force meeting in San Diego (Carol Bean, NCRR, Chair); each testbed is writing up notes on their experiences with/identified needs for ontologies, for a presentation to the BIRN Executive Committee. See FBIRN notes [[FBIRN:Ontology_Notes_March_2005|FBIRN:Ontology Notes March 2005]]
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Revision as of 13:26, 18 December 2006

Home < Mbirn: Updates

4/13/2005
Teleconference regarding Ontology development: Behavioral Domain improvements. Angie Laird and Jessica Turner present.

Action Items:

1) Beginning with Attention and Working Memory as the areas to flesh out in the Behavioral domains: Ask the experts (A. Belger responded re: attention already), and check the textbooks (Jess). With an updated taxonomy (Angie), Angie can pull out papers previously stored as "Attention" and improve their descriptions (this is a long-term goal, not by April 29). This serves as another method of validation.

Note that dividing Attention into "voluntary" and "involuntary" allows the distinction between the FBIRN Phase I MMN and the FBIRN Phase II Oddball to be represented in this dimension.

2) Jess will do a search of UMLS on attention and working memory to get a handle on how those concepts are represented (or not). She is also in contact with the Ontology Task Force regarding the relationship between the BIRN HID and the Mediator and how the ontologies are accessed; this will affect how the taxonomy being developed here is used to best advantage.

3) Take an FBIRN Phase I analysis done in SPM (e.g., the MMN data for the two subjects at UCI) and represent the final results of one contrast in the BrainMap Submit method (Jess, then Angie). The current description was a quick toy based on an abstract notion of the experiment and not driven by an actual table of MNI-space maximal clusters.

3) David and Angela will review the XML/ENT modifications from 4/6/2005.

4) Next call Wed April 20 at 8:30 am PDT.


4/6/2005

David sent the XML schema description we agreed on; Angela augmented the project-level descriptions to fit the BrainMap descriptive schema.

3/22/2005
Meeting at the FBIRN AHM regarding ontologies and BrainMap interactions. See Experimental_Taxonomy_Discussion


3/17 and 3/18/2005
Meeting at UCI between FBIRN and the San Antonio BrainMap representatives. Attendants: Jessica Turner, David Keator, Angie Laird, Angela Uecker. See FBIRN:BrainMap Discussion.


3/7/2005
Ontology Task Force meeting in San Diego (Carol Bean, NCRR, Chair); each testbed is writing up notes on their experiences with/identified needs for ontologies, for a presentation to the BIRN Executive Committee. See FBIRN notes FBIRN:Ontology Notes March 2005


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