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.  See the latest presentation on cbscentral on google slides.

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 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 for both the title and the Project Abbreviation. 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, use the "New" menu:

then fill in the relevant information on the new project page:

 

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. The general outline of steps is below.

It is possible to skip several steps in this pipeline. You should set the Project ID on the scanner when you register the subject - this avoids your session being put into limbo. Instead, your data is sent directly from the scanner to your project on CBSCentral. For complete directions, see here

You can also skip manual archiving completely. This is advisable for routine work on a study, once you have manually archived a session to set the scan types correctly. However many of the specialist fields for the scan session and subject will need to be filled in manually. See details here

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.Make sure to set the scan type to BOLD for any functional runs so that the automatic QC runs.

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 have my data go directly to my project for archiving?

When you register your subject at the scanner, you are required set the CBS Central Project ID. When this is done, then when you send the data from the scanner to CBS Central, it will appear in the pre-archive already with your project set correctly. You will still need to archive your data, but the step where you move it from limbo to your own project is not necessary.  

To avoid having your data assigned to limbo, when you register your subject at the scanner, enter the project ID in the Additional Info field, found right under subject height and weight. Use this format:

Project:your_project_id

Note, there is no space before or after the colon. See the figure below.

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 make a typo and enter a non-existent Project ID, the data will go to limbo and will need to be moved to your project prior to archiving.

Remember, you can semi-automate much of the registration process if the previous scan from your study is still on the scanner database (in the Patient Browser). Most of the registration fields can be pre-populated, which avoids having to contantly type (and typo) lengthy session name formats, and the Project ID information.

To do this, make sure the previous session in your study is highlighted in the patient browser, and then press the keyboard button for patient registration:

This results in the subject/session/demographic AND Additional Info from the previous session to be automatically populated in the Registration panel. Now, you only need to modify the demographic info for the new subject, and edit the session name for the new session:


In this example, just edit 190914_FIMMRI113_REC to, eg: 190918_FIMMRI113_REC, and update the age/sex/weight/height for the new subject. This avoids a lot of painful typing and typo-ing of session names and Project info. This is even more useful when the same subejct is being registered for multiple session, as you don't have to re-enter their demographic information each time.

 

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 only the 'owner' of a given project can turn on auto archive in CBScentral.

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.

 

Once the project has been configured to auto-archive, when data is sent from the scanner to CBS Central, all pre-archive and manual-archive steps are skipped. The data is automatically archvied in your project upon receipt of the DICOM's, provided you set the Project ID in the Additional Info field at patient registration:

Additionally, when auto-archiving, the following happens:

- The Patient_ID field on the registration window becomes the session name.
- The Patient's Last Name field becomes the subject name.

To comply with the Center's session naming policy, the Patient's last name must begin with YYMMDD_ . This may run afoul of your subject naming convention. In that case, CBS Central can use a subject name for archiving that is different from the Patient's Last Name on the registration panel. To do this, enter the extended string in the Additional Info field:

Project:your_project_id,Subject:CBSCentral_subject_name AA:true

The only space is between the end of the subject name and the AA:true. There are no spaces around the colons or comma.

Also when Auto-archiving, the scan type is set to whatever that scan name has been set to previously (if there is a record of this on CBS Central), otherwise a new scan-type is created which equals the scan name. To ensure BOLDqc runs correctly, you need to manually archive one session in your study to set scan type = BOLD where its needed, then this will be copied for auto-archived sessions.

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

The command for this is ArcGet.py. To get the command you need to load the yaxil module:

module load yaxil

Documentation on how to use Yaxil and ArcGet.py can be found at readthedocs.