Data Access

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The CNI has developed an integrated neurobiological image management system (NIMS) to facilitate the stewardship of all data collected at the CNI. NIMS is currently under active development. NIMS 1.0) 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. NIMS 2.0 is currently under active development; check the status on github page.

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

The Reapers: 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. The reapers are ever-running processes that reap images acquired on the MR scanner (cnimr). This process automatically copies all imaging data acquired on cnimr to the secure file server (cnifs) that's accessible via the WebAuth-protected site at [1]. In nims, the data are organized by the group name, an experiment name (both set at scan-time in the PatientID field), and exam date. Dicoms are archived in tar-gz files (one per acquisition) and are also converted to a NIfTI file (also one per acquisition). P-files are copied into this same folder, and P-files from our custom PSDs (e.g., spiral and SMS-EPI) are reconstructed and the resulting images saved in a NIfTI. Physio data, if recorded, are saved on nims as well.

Data Organization

Data acquired during a session can be automatically organized for you with a custom Subject Code by entering a "'sorting string'" into the PatientID field on the exam setup page.

The sorting string works as follows:

 <subject_code>@<group_name>/<experiment_name>


For example, the following string in the PatientID field would organize the given session into the "colorblind" experiment within the Wandell group, with the subject code of "ColorBlind_s83":

 ColorBlind_s83@wandell/colorblind


Please note the following:

  • While <subject_code> and <experiment_name> will be created at scan time, the <group_name> must match the Principal Investigator's SUNetID (e.g. wandell).
  • <subject_code> is not required and will default to the exam number.
  • If the sorting string is incorrect and can't be matched to a PI it will be placed into the unknown group and a CNI admin will need to help you retrieve and organize it correctly.

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.
  3. Your SUNETID must:
  4. Once the SUNET ID is created, email your SUNET ID the collaborating Stanford PI; he/she must give you permission to access the data.
  5. 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.
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