Raw Data

The first step in any image analysis pipeline is actually acquiring the data. After data is acquired at the scanner, it is pushed to a server called CBIHome.

You can read more about this process via the linked PowerPoint made by the CBI.

1. Downloading scan data from CBIHome

• Open Filezilla (or the FTP software of your choice)

• Enter the address to CBIHome (sftp://cbihome.musc.edu), as well as your NetID and password

• Navigate to the top level directory, then to MRData, then to your PI's folder, then to the study folder of your choice

• Download scans of your choice

  • Note that you can set the output destination for your downloads - set this to the folder on your desktop in which you will organize your newly downloaded data

2. Unzipping dicom folders

• You can unzip newly downloaded dicom folders in one of two ways:

  • Manually unzip the folders by double clicking (on Mac) or right clicking and extracting (on Windows)

  • Automate the unzipping process with a command line tool such as the bash tool 'unzip'.

    • See https://bridge-lab.gitbook.io/docs/general/onboarding/research-specialist-training#id-5.-workspace-setup for more details

    • To use bash unzip, open a Terminal and pass the following commands:

cd [filezilla download directory]
find . -type f -name '*.zip' -exec unzip {} \;

3. Sorting dicoms by sequence type

In order to access dicoms in a manageable way, they need to be sorted. This is done by looking at dicom meta data and sorting each dicom file based on a piece of meta data. There are many tools that allow a user to do this, such as simple-dicom-sort ( see https://bridge-lab.gitbook.io/docs/general/onboarding/research-specialist-training#id-5.-workspace-setup for more details).

Our study dicoms are typically sorted by series/sequence name - the name of the type of scan to which the dicoms belong. Below is the simple-dicom-sort command to sort a set of dicoms. This can be placed into a for-loop in bash to sort many subjects' dicoms at once.

dicom_sort [input] [output] %SeriesName%

4. Convert to nifti and BIDS format

See BIDS Data Organization.