Data Access

The CNI is developing an integrated neurobiological image management system (NIMS) to facilitate the stewardship of all data collected at the CNI. NIMS is currently under active development. A preliminary version of NIMS (NIMS lite) is currently deployed and used by all CNI users to securely access their scan data. This system is useful for organizing and archiving the data that users collect here.

The new version of NIMS is currently in beta testing. We suggest that all the CNI users give it a try. We will continue to run NIMS lite in parallel with the new version so that you can always go back there to get your data if something isn't working in the new system.

For more information on our NIMS software development efforts, see the CNI Software Development page.

mrReaper: Automatic data transfer to nims

A key part of NIMS is collating all data acquired in a scan session. A major aspect of that goal is already implemented and functional at the CNI. mrReaper is an ever-running processes that manage images acquired on the MR scanner (cnimr). This process automatically copies all imaging data acquired on cnimr to the secure file server (nims). From there, the data are available to all authorized users via the WebAuth-protected site at [1]. On nims, the data are organized by the PI's Name, an optional experiment name (both set at scan-time in the PatientID field), and exam date. All data acquired during an exam are put into a folder with a name of the form YYYYMMDD_EXAMNUM. Dicoms are archived in zip files (one per series) and are also converted to a NIFTI file (also one per series), if possible. P-files are copied into this same folder, and P-files from our custom spiral PSD are reconned and a NIFTI of the resulting images is also offered to the user. Physio data, if recorded, are saved on nims as well.

Data Sharing

This section describes the way in which data can be shared among researchers.

IRB Considerations

Before data can be shared across researchers the principal investigator responsible for the original data should make sure that provisions are in place within the approved IRB protocol that allow data sharing and assure that all requirements set forth in the protocol regarding data sharing are met.

Sharing data within the Stanford community

Persons seeking the data (PI or Lab Manager) should:

1. Find the data to be shared and note the experiment name, subject code, and session numbers.
2. Contact the principal investigator and officially ask for the data to be shared. Contact should be between PIs.

The persons responsible for the data (PI or Lab Manager):

1. Assure that the IRB protocol under which the data were collected allows for data sharing.
2. Log into [cni.stanford.edu/nimsgeard NIMS]
3. Navigate to the 'Manage Experiments' page
4. Find the experiment that will be shared
5. Drag the sunetid of the person with which you will be sharing the data over the experiment name and choose the permissions level you wish to grant.