Brain Imaging & Analysis Center

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BIAC Basics

=====  Getting started =====
Welcome to the BIAC Wiki!  This page will help you get started at BIAC and introduce you to the various systems for data analysis and otherwise.  You can also bookmark this page to use as a resource for common reference.

====BIAC User Access====

===BIAC User Access Instructions===

1)	**You __MUST HAVE__ a DHE account to gain BIAC access.** If you already have a DHE account, then you can go to the next step. If you do not have a DHE account, follow the steps found at: [[biac:accounts|Account Requests]] or [[http://wiki.biac.duke.edu/biac:accounts]]

2)	Email [[biac-newuser@duke.edu]] with your general access request and include:
  * Email 
  * NetID 

3)	BIAC will then create your record in REDCap.
  * If you need Level 1 Access, a New User Orientation will also be set up at this time. More information found here: [[biac:experimenter_sops|BIAC New User Orientation]] or [[https://wiki.biac.duke.edu/biac:experimenter_sops]]

4)	Once your record is created, an email will be sent from [[biac-newuser@duke.edu]] to the email address you previously provided.
  * Click on “BIAC User Profile” or the link to begin the survey

5)	Login to the survey using your NetID and email, and complete the survey.

6)	If you requested Level 1 Access, an additional email will be sent titled, “Level 1 Access Survey”  __**DO NOT begin this survey until you have:**__
  * Scheduled a New User Orientation
  * Completed the MRI Safety Quiz
  * Completed the MRI Level 1 Access Signature Sheet 
  * Completed the MRI Subject Screening form 

**The safety tutorials, safety quiz and both documents can be found here: [[https://www.biac.duke.edu/research/safety]]** 

7)	Upload both documents, the date you completed the MRI Safety quiz, and the date of your New User Orientation session in the Level 1 Access survey.
  * The Login for this survey is the also your NetID and email 

8)	Once you have completed the “BIAC User Profile” survey, the “Level 1 Required Training and Documents” survey (only if need Level 1 access), and the New User Orientation, your sponsor will be contacted to confirm your access request.

9)	Once your sponsor confirms your request, access will be provided.
 
===BIAC User Access FAQs===
Q: What is Level 1 Access? Do I need it? 
  * A:This access is for those who plan to bring participants to the scanner suites and/or use the test rooms. For Level 1 Access you will to complete the New User Orientation, the MRI Safety quiz, the MRI Subject Screening Form, and the MRI Level 1 Access Signature Sheet. 

Q: How do I schedule a New User Orientation?
  * A: Email biac-newuser@duke.edu and request a New User Orientation session. All sessions are currently taught over Zoom for approximately, 1.5 hours.  

Q: I only need access to an experiment’s data; do I need to complete a New User Orientation session? 
  * A: No. New User Orientation are for those requesting access to the scanner suites/test rooms and plan to work with participants. If you only need data access, please email biac-newuser@duke.edu with your access request, NetID, and email.

Q: I already have data access but need to get scheduling access, who do I email? 
  * A: Email biac-help@duke.edu with your access request with your sponsor CCed so your request can be confirmed. 

Q: Can I access the REDCap surveys from anywhere or do I have to be on the Duke network? 
  * A: The BIAC User Profile survey and the Level 1 Access survey through REDCap can be taken anywhere. You will just need to login into the quiz using the NetID and email you previously provided

Q: I now have access to the BIAC Scanner Schedule, but I cannot login to view it…
  * A: Make sure you are on the DHE network or on a DHE computer. If you are working remotely, you may need to request DHE access. Learn more about DHE access here: [[biac:accounts|Account Requests]]

==== BIAC administrative access ====
Setting up your BIAC accounts: http://wiki.biac.duke.edu/biac:accounts or [[biac:accounts|Account Requests]]

You will need a handful of accounts for full access to all of Duke and BIAC's resources.  Please pay close attention to the information needed when emailing requests.  It will make the set-up much smoother!

Also, please be aware of the training and certifications you need.  You can find the MRI safety information here http://www.biac.duke.edu/research/safety/ the HIPPA training here http://www.safety.duke.edu/ and the CITI certification here https://www.citiprogram.org/Default.asp?  Once this is done, make sure you lab has added you to their IRB's before you work on any data!

In order to gain access to specific studies, please email help@biac.duke.edu with the name(s) of the study and request that your PI verify the access as well.  You must also do this for BIAC calendar access.
==== Network ====

==Servers==
Hot off the scanner, your data will travel to purchased space on a server, such as "Munin" or "Fatt."  Your data basically lives here, but is analyzed on the cluster.  For more information on the scanner to server process, visit http://wiki.biac.duke.edu/biac:pipeline

On the server, each study has a respective study folder (see example).  In order to access this folder you must "map the drive."  Do this by selecting the "My computer" icon on your desktop, then the "map drive" icon at the top of that window.  Any drive (letter) can be chosen, then for the folder type the server, for example Munin, then the path, for example \\Munin\data\fbirn.  Check the "reconnect at logon" box and hit "finish."


==The Cluster==
Once you get a cluster account, you can set up access like so... [[biac:cluster:access|Accessing the cluster]]

You analyze your data by "submitting jobs," on the cluster, see [[biac:cluster:submit#job_submission|Job Submission]]
==== People ====
BIAC website: 
[[https://www.biac.duke.edu/people
]]

Affiliates:
CCN - http://www.mind.duke.edu/
DIBS - http://dibs.duke.edu/
{{section>[biac:analysis]#useful_guides}}
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