| Stage | Action | Data |
|---|
| Model Definition | Internal External Investigator defines model of interest and biomarker. Concept definition. | Project summary & Contact Info |
| CIVM project proposal | Investigator defines scientific goal, need for resources | -Project code -Local Investigator -External Collaborator related information -Nature of collaboration -Funding source |
| IACUC | Investigator defines -strain -no of animals -source -animal handling & procedures & drugs to be administered -imaging procedures -expected outcome | -Animal population information -Research Plan |
| Animal Preparation & Perfusion | Duke technician enters: -animal information: ID, age, sex, weight, date of arrival -appropriate metada-, perfusion details, drugs administered -These data go into the animal database | -Specific/Individual animal info -Animal preparation methods -Observations/Notes |
| Scan | -Standard coil, specimen position, image sequence, scan parameters -Duke investigator enters location in DUKE database where data needs to be archived, project code, animal ID -Image metadata extracted automatically from scan header and used in the recon and archiving steps. | -Scan parameters -Raw data |
| Reconstruction | Reconstruction of raw data to image | Image and reconstruction parameters |
| Archive Original Scans | Image data are stored together with animal data -quick view of image data from database html interface -Image and animal database are connected so one can query either | -Results of queries to either image or animal database -Directory structure |
| Post Process | T2 weighted image calculation, alignment to reference target | Derived image set (T2W) |
| Segmentation & Atlasing | Segmentation pipeline: incorporates skull stripping, registration, intensity normalization. (for details: Neuroimage. 2005 Aug 15;27(2):425-35. ) | Bit maps of segmented volumes, registration transforms |
| Morphometric analysis | Registration, surface generation, global and local shape analysis (for details Badea. A, in preparation) | Volume, area, shape info, variability info |
