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

Those seeking to gain access to data should FIRST contact the Stanford PI who is responsible for the data to request access. Requests should be made between PIs.
Persons seeking the data (PI or Lab Manager):

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.
3. Once permission is granted you can log into NIMS and download the data.

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 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.

Sharing data with collaborators outside of Stanford

Collaborators seeking to gain access to data should FIRST contact the Stanford PI who is responsible for the data to request access. If the PI agrees to share their data, then the collaborator and PI should do the following steps.

Outside collaborators

1. Set up a SUNetID by visiting Stanford Accounts and choosing 'Create' -> 'I do not have a university ID' -> 'Continue without University ID'
2. Follow the steps to create a SUNET ID and pick a password, etc.

Your SUNETID must:


• Be 3-8 characters long (lower-case letters and numbers only)
• Start with a letter
We recommend: FirstinitialLastInstitution e.g.: For Michael Perry @ Stanford sunetid = mperrysu For more info regarding SUNET IDs: http://itservices.stanford.edu/service/accounts/sunetids
1. Once the SUNET ID is created, email your SUNET ID the collaborating Stanford PI; he/she must give you permission to access the data.
2. After they have confirmed that they have granted you permission navigate to the NIMS interface, find the experiment with the data and drag it to the 'Download' icon.

Stanford PI

1. After your collaborator has requested a SUNET ID, sponsor his/her account by visiting the sponsorship page, entering the SUNET ID and following the prompts to sponsor a free account.
2. Go to the NIMS database interface and choose -> 'Manage Experiments'
3. Find the SUNET ID of your collaborator and drag it to the experiment containing the data you wish to share.
4. A popup will appear allowing you to choose the access level you wish to grant your collaborator. We suggest you choose read-only or anon-read.

Choosing a SUNET ID

Your SUNETID must:

• Be 3-8 characters long (lower-case letters and numbers only)
• Start with a letter

We recommend: FirstinitialLastInstitution

 e.g.: For Michael Perry @ Stanford 
 sunetid = mperrysu

For more info regarding SUNET IDs: http://itservices.stanford.edu/service/accounts/sunetids