CBSCentral

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It is a repository for data storage that runs on XNAT.  XNAT provides infrastructure for neuroimaging data management and data sharing.  See Tim O’Keefe’s presentation on CBSCentral (via Google Slides)

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Because CBS Central contains sensitive patient information, it is protected within the FASSE network. Therefore, access to CBS Central is restricted to the Harvard Neuroimaging Community and their collaborators.

1. The easiest way to get an account is to go to the CBSCentral website, which requires that you have a VPN connection to FASSE open.
2. After you have a secure connection, you can go to the website, http://cbscentral.rc.fas.harvard.edu.
3. From the front page, click on the Register link and fill out the form.
   • Enter the name of the PI or faculty member to whose lab you belong in the lab field. This is the person that will approve your account. If your PI does NOT receive an email to this effect, contact Jenn Segawa (jsegawa@g.harvard.edu).
   • You are also are encouraged to use your RC username as your CBSCentral login, BUT strongly discouraged from using your RC password.
   • Use a harvard.edu email address for the email.
4. Once you register, you will be able to log in, but will not be able to do anything else. In order to access or archive your data, you will have to be a member of your own lab specific project.

If you don’t have a RC account (or don’t know what that is) start with our Getting Started Guide.

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After requesting an account 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 the designated administrator for the PI, you should create a new Project.

Project Naming

Some PIs prefer one account for all their imaging project, however 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 “Jane Doe” PI, you may prefer a single 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 the study.

To create a project:

1. Use the “New” menu:
   
2. Fill out the relevant information on the new project page:
   
3. Remember to set the appropriate permissions. We recommend “Protected” since this allows users to request access relatively easily and still protects your data.
   

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In order to access data, or even add data, you must first have access to the project. If you are a PI/Faculty Member, please create at least one project. (Instructions to create a new project).

To access to a project:

• Click on the “Other Projects” link under the “Projects” navigation heading:
  
  You will see a list of projects which are visible but not yet accessible to you.
  NOTE: If you don’t see the project you’d like to access, it either doesn’t exist, or the PI who owns the project does not wish to have it publicly visible. If the later is true, you will have to contact them to ask for access.
• Find the project you would like to access. Click on the project’s ID or Title (blue text).
• Click on the Request Access link.
  
• You will then be prompted to enter some details around your access request:
  • Select “Collaborator” for read access, “Member” for read/write/archive access, or “Owner” if you want to manage access to the project.
  • Under Comments, tell the PI why you need/want access.
• Click “Submit Request” and the owner of the project will grant or deny your request.

If the PI does NOT receive an email regarding your request, contact Jenn Segawa (jsegawa@g.harvard.edu).

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There are 3 places your data could be sent:

Where it goes depends on what you entered in the “Addition info” box on the scanner console when you registered your participant:

• If it’s blank (or the information is entered incorrectly): the data will go to Limbo (how to retrieve it)
• If you enter the Project name (Project:project_ID), the data will go to the project’s pre-archive (how to archive it)
• If you enter both the Project name and AA:True (Project:projec_ID, AA:True), the data will go to the project’s archive.

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Don’t panic. It’s still there! It was just sent to the Limbo Project, and you don’t see it on the CBSCentral website, because you probably don’t have access to that project. This happened either because you didn’t enter the Project into the “Additional info” box when you registered the participant on the scanner, or because something was entered incorrectly.

If this happens, contact Jenn Segawa (jsegawa@g.harvard.edu), and she will help you get the data re-sent to your project so you can have access.

To prevent this from happening again, enter the project ID in the Additional info box when you register your participant at the scanner console. It is found right under “Height” and “Weight”. Use this format:
Project:project_id

Note that there is NO space before or after the colon.

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NOTE: You can also skip manual archiving completely. We recommend this 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 More on auto-archiving here.

The manual archiving process is illustrated below:

1. Go to the pre-archive area of CBSCentral website by pulling down “Upload” on the home screen:
   
2. In the pre-archive, find your session. You can sort the sessions by “Scan Time” (click twice) to bring the newest sessions to the top.
3. If there is a blue status notice on the right, your session is not ready to archive. If it says, “Ready”, highlight the session you want to archive by clicking on its row, and click “Archive”.
4. After clicking “Archive”, you’ll be taken to the session archive window. This lists information 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.
   
5. 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 demographic analysis, it is best to complete as many fields as possible.
   
6. 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.
   
7. 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.
   

Now you can download your data (via ArcGet.py) and view the automatic QC results.

There are two options to configure your project to auto-archive:

If you want your data to always auto-archive:

• On the CBSCentral website, click to your project from the “Projects” tab on the 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
  
• When you register the participant on the scanner console computer, set the Additional Info field to Project:project_ID
  • Note that there is no space before or after the colons, and project_ID is the ID code of the project, which you can find on the CBSCentral website.

If you want control over when your data is auto-archived:

You might want to choose this version if you’re not sure if your BOLD scans will be labeled correctly, or if you just prefer using this method.

• When you register the participant on the scanner console computer, set the Additional Info field at patient registration (on the scanner console) to Project:project_ID, AA:true
  • Note that there is no space before or after the colons, and project_ID is the ID code of the project, which you can find on the CBSCentral website.

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To transfer your scanner data to FASSE, you first need the following:

• RC account
• VPN connection
• CBSCentral account
• Access to the project

Then you begin to set-up your transfer. The command is ArcGet.py which is included in the yaxil module. Additional Yaxil and ArcGet.py documentation can be found at readthedocs.

First you will need to create two files.

1. Create .xnat_auth document and put it in your home directory (i.e., /n/fasse/users/your_RC_user_name folder) that contains
   
   <xnat>
<cbscentral version="1.5">
<url>http://cbscentral.rc.fas.harvard.edu</url>
<username>your_RC_user_name</username>
<password>superSecretPassword</password>
</cbscentral>
</xnat>
   
   replacing your_RC_user_name with your RC user name, and superSecretPassword with your RC password.
   
   You can either a) make this file on your own computer and transfer the file, or b) create an empty document and copy and paste the text in (via a Remote Desktop or via ssh).
   
   Note that if you look for this folder using the File Manager on your On-Demand Desktop, you won’t see it unless you change View -> Show Hidden Files to on:
   

2. You will also need to add a .yaml file to download your data in BIDS format.
   • This file can go where ever you like. We recommend putting it in your lab directory folder where you might store other scripts.
   • The file can be named whatever you like, we just recommend it has the .yaml extension so you remember what it is, e.g., your_study_name.yaml
   • Below is an example script: download link (txt)
     
     

• To adjust the file to your scan:
  • Edit the scan types; these are all in BIDS format.
    • Note: If you are using sbref, it should should be a different modality (aka like “bold”) listed under “func”.
    • If you would like to download DWI data, contact, Jenn Segawa (jsegawa@g.harvard.edu)
  • The scan numbers should match those from CBSCentral, not the scanner console.
    • If all your scans go perfectly, you will only need one yaml file for each study. However, if you have extra sequences, or the sequences are out of order for any participants, you may need to adjust the yaml file for each participant.
  • The task name should be the same across all the runs you plan to analyze together.
  • The id is only necessary if you use the intended for parameter.
    • This way, even if the scan numbers change, you don’t have to adjust other references to that scan.
    • This is particularly useful for fieldmaps; if you set this, fMRIPrep will automatically apply the fieldmap warping to any listed images.
    • If you have multiple sets of field maps (e.g. if you took the participant out the scanner halfway through a scan), then edit the intended for field so it only reflects the appropriate scans.
  • CAUTION: This document is sensitive to white space. For instance, if some of your indents include tabs but others are all spaces, ArcGet.py will fail.
    

Once you have the .xnat_auth and .yaml files set, open a terminal either using a Remote Desktop or via ssh, and type:

3. module load ncf yaxil
4. ArcGet.py -a cbscentral -p project_ID -l your_session_name -c your_study_name.yaml -o ./ -f bids
   • where project_ID is the project ID on CBSCentral, your_session_name is the Patient ID/Last Name in the Patient Registration on the scanner console, and your_study_name.yaml is the name of the yaml file you made in Step 2.
   • ./ will write the bids directory inside the current directory. Specify another path to a directory if you would like it somewhere else.
   • -f bids will write your data in BIDS format. Omit this flag if you want your data in a flat structure.