Center for Functional MRI In the Department of Radiology

Scanner Operations FAQ

  •  What can I do in Research Mode?

Research Mode enables the following functionality:

  • Non-product (e.g. home-grown) pulse sequences can be run safely in this mode. Popular spep for spiral 2D acquisition and ASL imaging, and field-map pulse sequences  require this mode in order to run.
  • For functional imaging protocols timing parameters, such as TR and # reps (and also blocking of on-off conditions) can be entered directly via fMRI screen.
  • When running functional scans, BrainWave RT (real time) GUI can be bypassed.
Back to Top
  •   How can I enable Research Mode?
Research Mode can be enabled/disabled via the System Preference window.  Click the the downward arrow on the TOOL button (the right most button of the triple button set on the top left corner of the screen), and select System Preference.  This step has to be done before the start of an exam. If an exam has already started, click on the downward arrow on the Scan Tab (The top right corner of the screen) and select Preference
Return to top
  •   I need raw data files (P-files) produced by regular GE ("product") sequences. How can I get them?
Make sure research mode is enabled. Save series by pressing Save Series button, and select Prep Scan. Go to Research CV page  and select Display CVs. In the CV name field type in autolock and set its value to 1. Close the CV window.
Return to top
  • When copying slice prescriptions from previous scan using "Copy RX "button in the Graphic RX screen, should I use "Present Loc" or "Original Loc"? They seem to be doing the same thing.
Original Loc should be used to copy the prescription from previous functional (fieldmap) scans to the current fieldmap (functional scan) prescription.
Return to top  
  • Should I use top-down or bottom-up phase encoding view order for fMRI?

The Center recommends bottom-up view order for fMRI. Using top-down view order may generate more gradient heating. However, top-down view order can be considerd for the following reasons:

  1. The geometric distortion has less impact to the region of the interest in top-down than in bottom up view order.
  2. More slices or better spatial coverage is needed while no other means can achieve that.

Phase encoding view order refers to the direction in which the Kspace is acquired. In top-down view order, acquisition starts from the topof the Kspace; whereas in bottom up view order, acquisition starts from the bottom of the Kspace. Please note that phase encoding view order is not the same as phase encoding direction. Phase encoding direction refers to the physical dimension in which the phase encoding gradients are applied, e.g. left-right, anterior to posterior, or superior to inferior. Each phase encoding direction can have either bottom up or top down view order.

Because Kspace is acquired in opposite directions in top-down and bottom-up, the off resonance effects in MRI images (e.g. geometric distortion, chemical shift) are opposite. A good example on the GE 3T scanners is: when acquiring axial EPI images in human with anterior-posterior phase encoding direction, bottom-up view order causes the voxels to shift towards the anterior, whereas the top-down view order shifts the voxels towards the posterior. The voxel shift causes either stretching or compressing of the targeted brain region. In general, stretching is preferred over compressing as stretching is easier to correct using field map correction algorithm.

Additionally, in GE's implementation of top-down view order, partial K space is always used (only the top half of K space is acquired). Whereas in bottom-up view order, full K space is used by default. Therefore more slices can be acquired in a same TR with top-down than with bottom up, providing bigger spatial coverage. The caveat of using top-down view order at the maximum slice/sec rate is that the gradient heating becomes more severe.

Back to Top
  • How do I save/load a protocol on MR750 using a USB drive?

Saving a Protocol on MR750 using a USB drive: pdf

Loading a Protocol on MR750 using a USB drive: pdf

Back to Top