MRI setup & programming

Varian 9.4T MRI Tips

  • EPI optimization

      • Shim volume should be inside the brain & away from the ear canal

      • Always use R-L as readout direction

      • Use ramp sampling to reduce echo train length

  • Data size limit

      • Maximum FID file size is 2GB

      • Which means for 10 slices of 256x256 image, you can only acquire < 410 repetitions (using single channel) or < 103 repetitions (using 4 channel).

      • If exceed, the scanner will run but no data will be saved! Have to calculate your data size if you plan to scan high-res and many repetitions.

  • Introduction to Varian system (PowerPoint)

Bruker Biospec 9.4T MRI Tips

  • Bruker Paravision training video

  • EPI optimization by MAPSHIM

      • Load Field Map protocol and run MAPSHIM macro to acquire field map.

      • Load PRESS protocol and use it to select the voxel for localized shim.

      • Run MAPSHIM with "Local" option.

  • Make new sequence

      • run /opt/PV5.1/bin/CopyMethod

      • make install clean cproto

      • copy *.ppg/*.mod files to /opt/PV5.1/exp/stan/nmr/lists/pp

      • restart PV to see the new sequence

  • Artifact

      • Dark bad in spin-echo:

        • cause: mismatched excitation and refocusing RF pulse bandwidth

        • solution: reduce exc bandwidth to make refoc bandwidth at 10-20% wider

    • "Motion" in phase-encoding direction of EPI

        • cause: frequency drift due to gradient heating

        • solution: reduce duty cycle by increasing TR or reducing number of slice

Bruker ClinScan 7T Tips

  • Orientation

      • Choose Head First, Supine to ensure the displayed orientation is like what it should be.

  • Optimize shimming for EPI

    • Display Adjustment volume (View->Adjustment volume) and reposition inside the ROI (eg, brain).

    • Choose Advanced shim mode in Sequence->Adjustment.

  • When "frequency adjustment doesn't converge"...

    • unplug and replug the coil connector

    • may need to do it a few times

  • Debug log files

    • Data, HostInstLog, HostLog, MRIRLog

Siemens 3T MRI Tips

IDEA programming Tips

  • Install sequence

      • copy *.dll & *.i86 to \MedComm\MriCustomer\seq (on host)

  • Gradient system

      • ClinScan: 7TZ

      • Trio: TQ-engine

      • Change gradient setting in IDEA: type 'gradconf -h' to see detail.

  • External RF file

      • \n4\MriSitedata\7TZ (or TQ-engine for Trio) (in IDEA)

      • \MedComm\MriSitedata\measurement (on host)

      • perform PAS unload in ideacmdtool every time you add an RF file

  • External gradient table for DTI

      • \n4\x86\prod\bin (in IDEA)

      • \MedComm\MriCustomer\seq (on host)

  • Get k-space data

      • open start menu by CTRL+ESC

      • Programs->Save Meas Data

      • look for data based on date/time

      • Option->copy from RAID

      • k-sapce data will be saved as meas.dat