OHBM Requirements

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The list below, roughly in order of priority, is a brief list of new caret_commands, with further descriptions of each command on it's corresponding wiki page. The names are considered place holders, to be modified and amended by Matt, David, et al. as needed. In parenthesis next to each command is the name of the developer assigned to work on the command, the expected completion date, and the current status (design/implementation/test/completed). Designate design if features are still being discussed, implementation for coding phase, test for test phase, and completed when the feature has been tested and verified working:



OHBM Requirements Proposed on 5/6/11

  1. Parcel_Constrained_Atlas_Resampling_and_Smoothing needed ASAP (JS) status: completed
  2. Parcel_Constrained_Smoothing needed ASAP (JS) status: completed
  3. Create_Cifti_Dense_Time_Series (needs test data location from Matt), needed ASAP (JS) status: completed
  4. Add support for Cifti File format to + bugfixes Metric_Correlation_Matrix_Cifti (needs test data location from Matt), needed ASAP (JS) status: completed
  5. (low priority for now) Create a Caret Command for converting Surface to FNIRT warp fields Surface_to_FNIRT, needed by ??? (JS or TC) status: design
  6. (low priority for now) Create a Caret Command for the calculation of an average parcellated dense time series Create_Average_Parecellated_Time_Series, needed by ??? (JS) status: design
  7. Display timecourses on a single chart instead of a new chart for each graph (JH)
  8. View single timepoint (from a Dense Time Series) on surface nodes and volume voxels. Must also allow sequencing through the timepoints (JH)
  9. Examine feasibility of displaying a web page (CDB) inside of Caret (JH)
  10. Create parcellated time series. Input is left/right label files and dense time series. Average rows with identical labels or subcortical structures (?) status: design

Needed by Dan's Group (from 3/31 meeting)

  1. Send Dan M. the CIFTI R-fMRI a pilot dataset, needed by 5/21/11 (MG) status: design
  2. Send Dan M. the CIFTI connectivity format reader/writer, needed by 5/21/11 (JS) status: design
  3. Create a Caret Command (or web service) to average one or more grey ordinates over an arbitrary group of Subjects Compute_Connectivity_Average needed by 5/15/11 (JS) status: design
  4. Connectome Workbench needs to be able to view downloaded CDB files, needed by 6/1/11 (JH) status: design
  5. Connectome Workbench needs to be able to query database and display results, needed by 6/1/11 (JH) status: design

OHBM Demo Technical plan

Below is a big picture overview of how both ConnectomeDB and ConnectomeWB will fit together for the OHBM demo, written by Dan Marcus.

OHBM 2011 Demo Technical Plan
April 4, 2011
Prerequisites: A version of caret command that computes dense connectome and outputs CIFTI for a specified list of subjects. (May 1, VE Lab)

1) User selects a subject group (May 1, NRG) Description: User identifies a subject group of interest by searching ConnectomeDB by subject attributes. User then clicks on “View in Workbench” link to visualize the subject group. This link downloads a file with some ConnectomeDB-specific extension (.cdb ???).

Requirements: Add a couple of synthentic subject attributes (hair length, hair color) to the KFC dataset. Add a “View in Workbench” button to UI. Define file format that is downloaded to Caret – will include the database URL and some way to identify the subject group (a group ID, search criteria, and/or list of subject IDs).

2) Subject group is loaded into Connectome Workbench (VE Lab) Description: When the .cdb file is downloaded, it is automatically opened in WB by registering the .cdb file extension to Workbench. When the file is loaded, a default atlas and default view are presented to the user.

Requirements: Method to link .cdb file extension to WB. File loading process in WB to read in .cdb file and load default atlas and view.

3) User clicks on a node to view group average connectivity. (May 8, VE Lab & NRG) Description: When a user clicks on a node of interest, WB submits a query to DB to retrieve the average connectivity.

Requirements: A DB web service to submit queries to. It should include attributes for the node # & hemisphere OR the voxel, subject group, and type of data (RS, DTI, some hybrid, etc; dense, parcellated; etc.) (NRG) Functionality in WB to submit appropriate query to DB. (VE Lab)

4) DB calculates the average connectivity. (May 15, NRG) Description: Based on the submitted query parameters, DB locates the appropriate CIFTI files and submits them as a list to caret-command.

Requirements: DB functionality to identify appropriate CIFTI files based on query parameter. DB functionality to call caret-command. DB functionality to cache generated CIFTI file.

6) DB returns the file generated by caret command. (May 25, NRG)

7) Caret display results. (June 1, VE Lab)

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