CBSCentral Questions

CBSCentral Questions

What is CBSCentral?

It is a repository for data storage that runs on XNAT.  XNAT provides infrastructure for neuroimaging data management and data sharing.  It will eventually contain several analysis streams that could be automatically run once data is entered into the system.

How do I get an account?

Because CBS Central contains sensitive patient information, it is protected within the NCF network. Therefore, access to CBS Central is restricted to the Harvard Neuroimaging Community and their collaborators. The easiest way to get an account is to go to the CBSCentral website, which requires that you either be sitting at a workstation or have a VPN connection to the NCF open. After you have a secure connection, you can go to the website, http://cbscentral.rc.fas.harvard.edu. From the front page, click on the Register link and fill out the form. Make sure to enter the name of the PI or faculty member to whose lab you belong in the lab field. In addition, you are encouraged to use your NCF username as your CBSCentral login, BUT strongly discouraged from using your NCF password. Once you register, you will be able to log in, but will not be able to do anything else. In order to archive your data, you will have TO BE A MEMBER OF LIMBO. See here for details on getting access to the limbo project and your own lab specific project.

How do I access data?

In order to access data, or even add data, you must first have access to a project. You will need access to Limbo (which is where your data initially goes when you push it to CBSCentral).  In addition, you will need access to your lab specific project. If you are a PI/Faculty Member, please create at least one project. Go here for instructions on creating a project. To gain access to a project, first, click on the “Other Projects" link under the “Projects” navigation heading:

 

You will then see a list of projects which are visible to you but to which you do not have access.

NOTE: If the project to which you would like access is not listed, then it either does not exists or the Primary Investigator who owns the project does not wish to let people know of its existence. If that case, you will have to ask him/her to grant you access by sending them an email. If the project is listed, click on it (in this example, clicking on Buckner):

 


You should see a page like the one below. Click on the "Request Access" link.

 

You will then be prompted to fill out some details regarding your access request like so:

 

You may then click on "Submit Request" and the owner of the project will grant or deny your access request.

 

How do I create a project?

After requesting a login and getting approved, you will normally be granted access to a project by the PI under whose name you requested access. However, if you are the PI or you are the designated administrator for the PI, you should create a Project. Normally there is one project per PI, however, this is just a convention and a PI may have any number of projects. We ask, however, that you name new projects using the PI's name for ease of identification. So for the average "Jane Doe" PI, the convention is to create one project named "Doe", or, if you'd prefer to have more than one project "Doe-ProjectName1", "Doe-ProjectName2", etc. where ProjectName1 is a name of your liking. To create a project, simply go to the new project page available from the "New" menu: Then fill in the relevant information.

 

And remember to set the appropriate permissions. We recommend "Protected" since this allows users to request access without much difficulty yet still protects all of your data.
 

How do I archive my data on CBSCentral?

Before your data can be accessed for analysis on the NCF, it needs to be archived on CBS Central.

Automatic archiving is possible if you have configured your project to accept sessions this way, and complete extra fields in the patient registration window at the scanner  - see details here. This is advisable for routine work, however many of the specialist fields for the scan session and subject will be auto-filled. If you are carefully tracking demographics, or trialing new protocols, this may not be optimal for you. The manual archiving process is illustrated below:

Begin by going to the pre-archive area of CBS Central by pulling down "Upload" on the home screen:

Once in the pre-archive, sort the sessions by "Scan Time" (click twice) to bring the newest sessions to the top. Then find your session. If your data is listed as Project Limbo, then before you archive it, it must be moved into your project. If you archive directly into Limbo you will get an error message. If you would like to avoid this step, you can have your data go directly to your project prior to archiving. To do this, you need to enter information at the scanner when you register your subject, see here for directions. To move your data from Limbo, highlight it by clicking on it, and click the "Change Projects" button on the right.

Moving the session to your project area (created above) is crucial, otherwise you will not be able to access the data after archiving. After clicking "Change Projects", a pop-up window appears, which allows you to choose the project, and then click "OK".

The move process takes a minute or two per session, so if you have more than one session to move, its a good idea to do them all at this time. When you have finished moving all sessions, refresh the pre-archive by again choosing "Go to Pre-archive" from the "Upload" menu option at the top of the screen.

Once you moved your data (or had the scanner send your data) to your project, you will need to go back to the pre-archive. Sort by session date (or project, if you like), to find your sessions again. Those with a blue status notice at right are not ready to archive, but those with the "Ready" notice are suitable for archiving. Highlight the session you want to archive, and click "Archive".

After clicking "Archive", you'll be taken to the session archive window. This lists informtation about the subject, sessions, and scans. All the fields with bold labels should be completed, fields with a red outline need to be completed before archiving will proceed.

If you have previously scanned this subject, you can enter the first few letters of their subject ID, and then select their ID from the options provided in a menu that appears below the subject field. If this is a new subject, then click "Add Subject". A pop-up window appears, in which you can enter the subject's information. Most of these fields don't have to be completed - you'll get a warning message but are able to proceed if leave fields blank. However, for full demograhic analysis, it is best to complete as many fields as possible.

Clicking "submit" will close the pop-up window. Other fields relating to the session should be completed. Pull-down choices appear for most of these fields.

Generally, the Scan Type fields will self-populate, and you will not need to do anything here. However, if any fields have a red outline around "Select", a pull-down choice must be used before archiving can proceed.

When all thse steps are complete, click the "Submit" button at the bottom of the screen. The archived session page will appear in a few seconds, indicating the session is being archived. You will receive an email when the archiving is complete - usually in a couple of minutes.

How do I skip limbo and have my data go directly to my project for archiving?

You can shorten the number of steps it takes to archive your data by skipping over limbo completely. You will still need to archive your data, but the step where you move it from limbo to your own project will no longer be necessary. If you would like to shorten the process even more, you can have your data auto-archived via these instructions, however this will not fill in any biographical information about your subject, and details about the scanner and such will still have to be entered manually. To just skip limbo and still manually archive, you enter extra information when you register your subject at the scanner. In the Study Comments field, you need to enter:

Project:your_project_id

There is no space before or after the colon. See the field with the red arrow below.

To get to the study comment, register your participant as usual. After you hit exam, you will see the something that looks like this:

Click on "Add Study Comment" in blue, it brings up a second box. Enter the information there.

To find out your project id, you can check CBSCentral. When you first login to CBSCentral, you will see a list of your projects. Each project has a name in blue, and then a Project ID in black below it. The Project ID is usually shorter, and will not contain spaces. For example, if I wanted to send data directly to Ross's Mair_MR_Physics project, I would enter Project:Mair. If you enter an incorrect Project ID, the data will go to limbo and need to be moved to your project prior to archiving.

How do I set my project to auto-archive my data?

 

You can avoid most of the steps of manually archiving your sessions above if you configure your project to auto-archive sessions, and then add the neccesary information in the patient registration panel at the scanner before each session begins.

Note that auto-archiving is advisable for routine work, however many of the specialist fields for the scan session and subject, which the user enters manually during the manual archiving process, will not be auto-filled. Subject details, demographics information, and scanner and coil information will need to be entered later after the session has archived. If you are carefully tracking demographics, or trialing new protocols, this may not be optimal for you

To configure your project to auto-archive, click your project from the "Projects" tab at left if necessary, and then click the "Manage" tab. Make sure the Prearchive Settings option is toggled to "All image data will be placed into the archive automatically" and click the Save button if necessary.

 

 

 

 

 How do I get my data from CBSCentral to the NCF?

The command for this is ArcGet.py. It should be in your path if you are using the default environment. To verify, type:

ArcGet.py -h

 If it is found, it will spit out the usage file that tells you all the flags for use. If not, please contact Stephanie (smcmains [at] fas [dot] harvard [dot] edu) to make sure your environment is setup correctly.

Before you run ArcGet.py, you will need to create the configuration file it uses.  This can be done via a script, which takes your username, and the information about CBSCentral and creates .xnat_auth, a hidden file in your user directory (~./xnat_auth).

xnat_auth --alias cbscentral --username your_cbscentral_username --url http://cbscentral.rc.fas.harvard.edu

This will prompt you for your CBSCentral password. Once you run this, you won't have to run it again.  You will just use the alias name (cbscentral) you set up in the call of ArcGet.py.

ArcGet.py -a cbscentral -s mri_sessionid -r 1,2,MPRAGE,BOLD

The -r flag allows you to specify which runs you would like to download. This can be done by either specifying either the run number (1,2,3) or the type (MPRAGE, BOLD), or a mixture of both. This is more important now that the extended BOLD QC is run on the data, as it creates a lot of misc files you don't want to download.

Some people may be using cbsget to access their data. This is a wrapper for ArcGet.py that may become unsupported in the near future. It works essentially the same, however it saves and reads your username and password from a separate file called arget.conf inslide of the hidden directory .xnat.d (~/.xnat.d/arget.conf).