Post-Scan Data Transfer

At the end of your scan session, you will need to copy your data from the scanner to one of the CFMRI supported servers (fmri1, fmri2, fmriserver, cfmri, etc.)

The current recommended method for copying data is “cfmricp”

cfmricp

To use cfmricp, open a command window on the scanner GUI and enter the command:

cfmricp

A MATLAB script will be initiated and you will be prompted to enter important information about your scan session

Session #  Start                 End                   Duration   Protocol                    Coil
1          14-Jan-2021 11:54:03  14-Jan-2021 12:41:23  00:47:20   Example_Protocol            RM:Nova32ch
2          14-Jan-2021 13:51:00  14-Jan-2021 15:51:00  02:00:00   CFMRI_Protocol              RM:Nova32ch

Choose your session # (blank will select the latest):

When prompted to do so, enter the session number of the scan session you wish to transfer

A log life will be generated (and printed in the command window) indicating which files will be transfered

*****************************************************
Session
*****************************************************
Initiation Date: 14-Jan-2021 13:55:30

Protocol:   Example_Protocol
Coil type:  RM:Nova32ch
Start time: 14-Jan-2021 11:54:03
End time:   14-Jan-2021 12:41:23
Duration:   00:47:20

*****************************************************
DICOMs
*****************************************************
p folder: p2695
exam #: e3150
patient id: test_subject12
s29306: 3Plane Loc SSFSE
s29307: ASSET cal
s29308: Screen Save
s29309: Sag MPRAGE T1
s29310: PU:Sag MPRAGE T1

*****************************************************
P-files
*****************************************************
No single band P-files were detected.

No multi band P-files were detected.

*****************************************************
NIFTIs
*****************************************************
No NIFTI files were detected.

*****************************************************
Physios
*****************************************************
No physio files were detected.

*****************************************************
Misc Files
*****************************************************
No miscellaneous files were detected.

The cfmricp code is a very useful tool and will grab all relevant files associated with your scan session:

  • DICOM data
  • ASL P-files
  • Multiband reconstructed nii.gz files
  • Physiological recordings

All of the relevant data is gathered from various locations on the scanner and sent with your final transfer

You should verify that the files listed in the log are consistent with the data you expect to receive from your scan session

The next step is to decide whether or not you want to proceed with the transfer

Do you want to proceed with file transfer?: y/n [n]

Assuming you answered yes (“y”), you will be prompted for the details of the server and username you intend to transfer to

Enter cfmri server name (e.g fmriserver): fmri2

Enter user id: ajacobson

After providing this information, you will be asked to define the “destination directory”

The cfmricp code will always default to sending data to the ~/data directory of your user account

If you would like the data from your current session to be transfered to the ~/data directory (common), you can simply provide the subject ID or scan session identifier specific to your study

Enter destination directory name under ~/data/: test_subject12

If you need to send the scan data into a more specific location within the ~/data directory of your server account, you will need to provide the path to the destination, followed by the subject identifier

Enter destination directory name under ~/data/: ExampleStudyDirectory/test_subject12

Using cfmricp Across Multiple Back-to-Back Scan Sessions

One potential issue with cfmricp is that it groups sessions by protocol, not exam

If the same protocol is used for 2 different subjects, with no scans between them from other imaging groups, cfmricp will lump all of the data into a single directory

The cfmricp_log.txt (created and sent with your cfmricp transfer) file will provide you with all of the appropriate info required to manually split the directory into multiple subject directories

Fortunately, there is an easier method to ensure you are only transferring the data from your intended MRI session

Simply use the following version of cfmricp

cfmricp_adj

And follow the additional prompts

Please list the START time of your scan session in 24hr format
(Enter exactly like this example: 29-Oct-2020 21:00  ):

Please list the END time of your scan session in 24hr format
(Enter exactly like this example: 29-Oct-2020 22:00  ):

After entering the date and time of the start and end of your scan session, the cfmricp code will proceed to the original prompts listed above, and only data from within the requested time frame will be transferred

If you have any issues or questions, please contact: Aaron Jacobson (ajacobson@ucsd.edu) and Conan Chen (coc004@ucsd.edu)