Data Access: Difference between revisions

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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 ([https://cni.stanford.edu/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 CNI uses [https://flywheel.io Flywheel] for data management and access. Please see the [[ Flywheel | Flywheel ]] page for more information regarding data access via Flywheel.
 
The [https://cni.stanford.edu/nimsgears/ 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 [[NIMS | 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 [http://webauth.stanford.edu/ WebAuth]-protected site at [https://cni.stanford.edu/nims/]. 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 =  
= Data Sharing =  
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== Sharing data within the Stanford community ==
== 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.''<br>
'''Persons seeking the data (PI or Lab Manager):'''
'''Persons seeking the data (PI or Lab Manager):'''
<ol>
<ol>
# Find the data to be shared and note the experiment name, subject code, and session numbers.
# Find the data to be shared and note the experiment name, subject code, and session numbers.
# Contact the principal investigator and officially ask for the data to be shared. ''Contact should be between PIs.''  
# Contact the principal investigator and officially ask for the data to be shared. ''Contact should be between PIs.''  
# Once permission is granted you can log into [http://cni.stanford.edu/nimsgears NIMS] and download the data.
# Once permission is granted you can log into [https://cni.flywheel.io Flywheel] and download the data.
</ol>
</ol>
'''The persons responsible for the data (PI or Lab Manager):'''
'''The persons responsible for the data (PI or Lab Manager):'''
<ol>
<ol>
# Assure that the IRB protocol under which the data were collected allows for data sharing.
# Assure that the IRB protocol under which the data were collected allows for data sharing.
# Log into [http://cni.stanford.edu/nimsgears NIMS]
# Log into [https://cni.flywheel.io Flywheel]
# Navigate to the 'Manage Experiments' page
# Find the experiment that will be shared
# 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.
</ol>
</ol>


== Sharing data with collaborators outside of Stanford ==
== 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.  
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 seeking access to data:'''
'''Outside collaborators'''
<ol>
<ol>
# Set up a SUNetID by visiting [http://accounts.stanford.edu Stanford Accounts] and choosing 'Create' -> 'I do not have a university ID' -> 'Continue without University ID'
<li>Set up a SUNetID by visiting [http://accounts.stanford.edu Stanford Accounts] and choosing 'Create' -> 'I do not have a university ID' -> 'Continue without University ID'</li>
# Follow the steps to create a SUNET ID and pick a password, etc.  
<li>Follow the steps to create a SUNET ID and pick a password, etc. </li>
# Once the SUNET ID is created, email the PI from whom you were given permission to access the data and provide them with your SUNET ID so that they may sponsor your account and give you access to the data.  
:Your SUNETID must:
# Once the PI with control of the data confirms that they have granted you permission to download the data navigate to the NIMS interface, find the experiment with the data and drag it to the 'Download' icon.
:*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
 
<li> Once the SUNET ID is created, email your SUNET ID the collaborating Stanford PI; he/she must give you permission to access the data.</li>
<li> After they have confirmed that they have granted you permission navigate to the Flywheel interface, find the experiment with the data and 'Download' those data </li>
</ol>
</ol>


'''PI with control of the data:'''
 
'''Stanford PI'''
<ol>
<ol>
# Once the SUNET ID for your collaborator is setup you should sponsor his/her account by visiting [http://sponsorship.stanford.edu the sponsorship page], entering the SUNET ID and following the prompts to sponsor a free account. Your admin can help with sponsorship issues, should they arise.  
# After your collaborator has requested a SUNET ID, sponsor his/her account by visiting [http://sponsorship.stanford.edu the sponsorship page], entering the SUNET ID and following the prompts to sponsor a free account.  
# Go to the NIMS database interface and choose -> 'Manage Experiments'
# Go to the NIMS database interface and choose -> 'Manage Experiments'
# Find the SUNET ID of your collaborator and drag it to the experiment containing the data you wish to share.  
# Find the SUNET ID of your collaborator and drag it to the experiment containing the data you wish to share.  
# Within the popup, choose the access level you wish to grant you collaborator.  
# 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.
</ol>
</ol>

Latest revision as of 23:16, 4 December 2019

The CNI uses Flywheel for data management and access. Please see the Flywheel page for more information regarding data access via Flywheel.

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 Flywheel 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 Flywheel

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:
  3. Once the SUNET ID is created, email your SUNET ID the collaborating Stanford PI; he/she must give you permission to access the data.
  4. After they have confirmed that they have granted you permission navigate to the Flywheel interface, find the experiment with the data and 'Download' those data


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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