Table of Contents

WebDB Help

Extract Data

After registering, running your scan and sending all your data sets, log into webdb and click on the session you just completed (n.b.: you cannot access the data before the end time you indicated when reserving the session.) and click on the View link. You will be shown the following page that displays the series with a check box next to each series. Select the series you would like to extract.

List Series

Save will take you the reconstruction page.

Conversion Options

Chose an Output Disk. You will notice a pull-down menu next to Disk. It will look something like this:

Output Disk

Any option starting with a capital name and colon, in this case "LARMOR:", indicates a disk on a remote machine. All other options indicate disks on the CBI file server. Here the Heeger lab is used as an example, each user will only see a list of disks that they have access to. The list can and will be modified when needed.

Fill in the Output Directory value.

Output Directory

You can specify a directory tree to create nested directories, e.g.: my_data/july1/first_run. Click on the Default button if you want to use the default directory (the accession number).

Organization indicates whether you want the data all in one directory or you want to split it with the data from each series in a different directory.

Unwarp images refers to the gradient non-linearity correction. It creates a folder called "unwarped" in each of the series with the unwarped version of the images. Use this option if you want to register images across different sessions (different subject positioning). For more information see CBI’s Gradient non-linearity correction paper (username and password required).

Siemens Data Format

If you selected any Siemens data (online reconstructed) you will see this section. The Siemens Data Format can be converted to a DICOM or NIfTI file, where the NIfTI file can be either single (.nii) or dual (.img + .hdr), and compressed or uncompressed. All conversions will include a ".txt" file which is a dump of the DICOM header of the first slice.

BIDS

BIDS Output

By selecting BIDS the output will be organized according to Brain Imaging Data Structure standard.

Disk and Output Directory follow the same rules as the other output options with one caveat: remote machine disks are not allowed

The subject field is automatically filled with the CBI subject ID stored in the data base. It can be changed to fit your format. The subject ID must be alphanumeric and any character that is neither a digit or a letter (lower or upper case) will be removed from the output.

The session field is blank by default. It can be filled with an alphanumeric entry. Any character that is neither a digit or a letter (lower or upper case) will be removed from the output.

Users can use their own classification scheme by storing it in a file called CLASSIFICATION.TXT. The scheme will be applied to the data at the same directory level or lower of where the file is stored. If the file is stored in a specific session, it will only apply to that session; if it's in a subject's directory it will apply to all sessions for that subject; if it's in a study it will apply to all subjects in that study; etc. The highest level that will be consireded is the top-level for each lab: /CBI/UserData/labname.
You can force the use of the default classification by selecting the appropriate check mark at the bottom right.