Mbirn: Updates - Revision history

Andy: Update from Wiki

2006-12-18T14:01:24Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T14:01:22Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T14:01:21Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:26:23Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:26:22Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:26:20Z

Update from Wiki

New page

'''Jan 17, 2005''' (J. Turner)

* Below are the minutes from our Jan 17 2005 teleconference (Steven Rao, Vinay, Jessica Turner, Gary Glover, Jorge Jovicich)
* Two starting projects were outlined for BIRN - Med College Wisconsin collaborations:

** '''Use of MCW fMRI data to drive fBIRN analysis tool developments'''<br />[[Media:Binder_-_Journal_of_Neuroscience%2C_1997.pdf|Binder et al. 1997]][[Media:Frost_-_Brain%2C_1999.pdf|Frost et al. 1999]]<br />
*** ''Actions:''
**** The next step is a teleconference with Jeffrey Binder, Greg Brown, Lisa Kilpatrick in early March to discuss dataset details. By early April we should be able to show progress and a timeline.
** '''Characterization of MCW's magnet stability using fBIRN's protocols'''<br />
MCW is currently taking possession of a short bore 3T GE scanner, and can use the FBIRN agar phantom protocol as a measure of the GE's stability and temporal dynamics. GE has seen this before, since UCSD used the same standards. FBIRN will send MCW an agar phantom as soon as they are delivered (currently ordered); in the meantime, MCW can start with the doped-water version of the 17-cm spherical phantom they have. <br />
*** ''Actions''
**** The next step is for FBIRN (Jess) to send Vinay the FBIRN agar/stability phantom protocol, using the Phase II version, as well as the agar recipe and the analysis methods.('''DONE''')
**** MCW (Vinay) will collect the data and share the results with the FBIRN (via Gary).
** Other projects discussed but not proposed for immediate action included possible interactions with Ted DeYoe (MCW) who has a legacy dataset of multiple subjects studied multiple times for retinal mapping; interactions with MCW in the development of the Smart Phantom, as proposed by the FBIRN in their renewal; and comparing Siemen's B0 mapping that FBIRN is using as part of their Phase II protocol, which dovetails with the FSL-standard correction method, with the methods MCW has developed.
----
[[MBIRNCollab-GCRC|mBIRNCollab-GCRC]]

@@ Line 1: / Line 1: @@
-'''Feb 24, 2005''' (J. Sacks)
+Teleconference regarding Ontology development: Behavioral Domain improvements. Angie Laird and Jessica Turner present.
-<br />'''Revised summary:'''
+Action Items:
-* 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.
+) 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.
-* 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.
+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.
-# 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.
+) 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.
-<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>
+) 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.
-* (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>
+) David and Angela will review the XML/ENT modifications from 4/6/2005.
-<br />'''Milestones''' for GCRC meeting in April:
+) Next call Wed April 20 at 8:30 am PDT.
-* (a) Results of investigation into which registration methods should to be used in Ibrowser
+<br />'''4/6/2005'''<br />
-* (b) A more refined definition of the project
-* (c) A revised workplan
+David sent the XML schema description we agreed on; Angela augmented the project-level descriptions to fit the BrainMap descriptive schema.
 ----

@@ Line 1: / Line 1: @@
-'''Feb 24, 2005''' (J. Sacks)
+'''4/13/2005'''<br /> Teleconference regarding Ontology development: Behavioral Domain improvements. Angie Laird and Jessica Turner present.
-<br />'''Revised summary:'''
+Action Items:
-* 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.
+) 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.
-* 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.
+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.
-# 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.
+) 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.
-<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>
+) 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.
-* (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>
+) David and Angela will review the XML/ENT modifications from 4/6/2005.
-<br />'''Milestones''' for GCRC meeting in April:
+) Next call Wed April 20 at 8:30 am PDT.
-* (a) Results of investigation into which registration methods should to be used in Ibrowser
+<br />'''4/6/2005'''<br />
-* (b) A more refined definition of the project
-* (c) A revised workplan
+David sent the XML schema description we agreed on; Angela augmented the project-level descriptions to fit the BrainMap descriptive schema.
 ----