Center for Functional MRI In the Department of Radiology

Announcements 2018

June 11, 2018

This notice pertains to the data handling of CFMRI MB fMRI/DTI protocols.

As of today, the raw data (P-files, .dat files) will stay in the S3 Bucket for three days before being archived to a CFMRI backup server. Therefore, if you opt to save the raw files, it is important to copy them from the bucket within three days after your scan session.

The reconstructed NIFTI files will be available on the scanner and can be transferred out using the 'cfmricp' command along with the DICOM/physio files.

Note that if you need to copy the NIFTI files from the bucket, the same three-day policy applies.

By now all MB users should have direct access to the S3 Bucket. If not, please contact David Shin (ddshin@ucsd.edu) for further assistance.

May 16, 2018

As part of the Center's OceanX initiative, we are making realtime recon available for CFMRI MB fMRI/DTI protocols on both 3T systems.

Users are no longer required to move large data from the scanner and run offline reconstruction, which incur heavy use of CPU/memory resources and hours of processing time.

At the end of each MB scan, your P-file and associated .dat files will be archived automatically and a reconstruction job will be initiated with powerful compute resources, which will return the reconstructed NIFTI files to the scanner computer (/export/home/007) in minutes (DTI: about 10:00 minutes; fMRI: about 15 to 20 minutes).

One of the major benefits of this new option is the ability to review your data on the scanner. During your session you will have the ability to assess quality and determine if a rescan is required within the same session.

As before, your DICOM and NIFTI files can be transferred out to your account on CFMRI servers (e.g. cfmri, fmriserver, fmrimems, fmri2) using the ‘cfmricp’ command. If desired, your P-files and .dat files will be made available for retrieval from an archived repository for up to 3 months.

Over time, our plan is to build on this capability to offer additional processing solutions to our users.

A couple of side notes:

  • When we upgrade our 3T systems to the latest software (DV26)/hardware, we are likely to transition to vendor supplied real-time recon solutions for most multiband protocols.
  • If your last run of the session is a MB fMRI, please note that it can take up to 20 minutes before it becomes available for cfmri cp transfer. The CFMRI tech staff is happy to help if your NIFTI files are missing.

Please contact Aaron or David for any questions or concerns.