Education, tips and tricks to help you conduct better fMRI experiments.
Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Wednesday, March 27, 2013

Quick update for Siemens users

Apologies for the lengthy absence. Many irons in the fire, etc. So until I can provide a more considered post I give you these three random tidbits:

1. Syngo MR version D13 for Verio and Skyra

There is an EPI sequence in VD13 that has a real time update of the on-resonance frequency, i.e. one that is computed and applied TR by TR, to combat drift caused by gradient heating. There are apparently versions for fMRI and diffusion-weighted imaging. I don't have any detailed information but if you are working on a Verio or a Skyra it might be time to talk to your physicist and/or local Siemens rep.

2. Phase encode direction for axial and axial-oblique EPI

Siemens uses A-P phase encoding by default whereas GE uses P-A by default. Essentially, for axial (and axial oblique) EPI the A-P direction compresses the frontal lobe but stretches occipital lobe whereas P-A stretches frontal lobe and compresses occipital. Pick your poison. (See Note 1.) Test each one out by setting the Phase enc. dir. parameter on the Routine tab. To set P-A from A-P (default) first click the three dots (...) to the right of the parameter field and open the dialog box, then enter 180 <return> instead of 0. You will probably find that the parameter change doesn't "stick" for appended scans, so saving a modified protocol in the Exam Explorer is a way to ensure the default (A-P) doesn't get reinstated without you noticing. More details to come in the next version of my user training/FAQ document.

3. Another way to force a re-shim

In my last user training/FAQ document (and here) I gave a simple way to force the scanner to re-shim at any point, e.g. when you know or strongly suspect the subject may have moved, or between lengthy blocks as a way to maintain high quality data in spite of slow subject motion and scanner drifts. But there is another way to do it and from some basic tests it looks to be superior. Here's a shaky video of the procedure conducted on a Trio running Syngo MR B17 (see Note 2):

(The essential procedure is the same for later software versions, but the layout of the 3D Shim window is slightly different.)