CivetOnCbrain

CBRAIN Interface

• At any time, you can obtain help about the Cbrain interface here https://wiki.cbrain.mcgill.ca/cbrain/cbrain.
• To start a CIVET project, login to Cbrain at https://portal.cbrain.mcgill.ca/login, click on “Create Project.”

• Name your study whatever you like (here, we chose “Example”).

• You will see a box appear below with your study name. Click on it.

• To upload a single file at a time, click on “Upload File.” To upload multiple files at one time, you may prefer to use an SFTP client; see https://wiki.cbrain.mcgill.ca/cbrain/uploading and downloading large files

• Browse to a folder to select a mnc file to upload. Here, we choose “sample_0001_t1.mnc.”
• You may leave the defaults to automatically detect filetypes, or you may manually designate them (e.g., Minc2)

• The file will be uploaded in a few seconds or minutes; you may perform other operations freely while you wait.

• You will be notified when it is done uploading.

• Repeat this for any other files that you wish to add.

• Check the files that you wish to analyze (either separately, or the top box will select everything).

• Click on “Launch Task,” and then on drop-down menu, “Select a task to launch.”

• Choose “Launch Civet.”

• Choose an execution server. We recommend that once you choose one, you consistently use the same one for all future analyses with the same dataset. Then click on “Launch Tool.”

• If you are a new user, you may want to leave many of the defaults.
• However, you will need to choose an “N3 distance” value. The N3 value that is optimal for your particular dataset may vary, and we highly suggest running a subset of your data at a few N3 values (at separations of ~25mm) in order to determine - based on visual quality control - which yields the most homogeneous intensity field. For 3T data, you may want to start with 125mm or 100mm, though it would be useful to also try 75mm and 50mm. For 1.5T data, you may want to start with 200mm. In this example, we used 100mm.
• Click on “Show” for “Optional post-CIVET operations,” and give your study a name. Here, we used “Example.”
• Be sure to check “Launch Claude’s QC script.”

• You will see CIVET appear under your “Tasks” tab. You will be notified when processing is complete, and you may perform other operations freely while you wait.

• When you have been notified that the tasks are complete, you may find your results under the “Files” tab, labeled as “Civet Output.”

• You may quickly view your output directly on Cbrain by clicking on a “Civet Output” filename (though this may not be necessary if you wish to download your data and do quality control directly on your computer, or on Brainbrowser; for more information on QC and Brainbrowser see: http://www.bic.mni.mcgill.ca/ServicesSoftware/QualityControl)

• Next, click on “Show Displayable Contents.” For more information on how to conduct Quality Control, click here: http://www.bic.mni.mcgill.ca/ServicesSoftware/QualityControl

• It will likely be necessary to use SFTP to transfer the files locally to your own computer. Check the boxes for the new output files. Click on “File Management,” under “Move/Copy” select “SFTP-Brainstorm,” and click on “Copy Files.” Please go here for additional instructions on using SFTP with Cbrain: https://wiki.cbrain.mcgill.ca/cbrain/uploading and downloading large files

• You will be notified when the transfer is complete, and you may perform other operations freely while you wait.