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.)

Here are the steps:
  1. Ensure the scanner isn't already running and also that a scan is open (i.e. "working man"), ready to go.
  2. Select the Adjustments option in the Options menu.
  3. Click the 3D Shim option towards the bottom of the Adjustments window.
  4. Start the field map shim by clicking the Measure button, towards the top right. It takes ~30 sec to acquire; you'll hear the scanner buzzing.
  5. Click the Calculate button (middle right) to compute a new set of shims from the new field map. (If you accidentally click twice or more the same calculation is performed.)
  6. Apply the new shims by clicking the Apply button towards the bottom right of the window. (Ignore any other Apply button(s) farther up if you have them, they relate to other adjustments. If you have more than one, go for the one that's nearest the bottom of the screen.)
  7. Close the Adjustments window.
  8. Start your next scan. (In the video I start a GRE sequence - actually a field mapping sequence - but any sequence can be acquired next.)

That's it! What's more, running this procedure after a Standard shim is equivalent to running an Advanced shim, except that the total time to do the Standard shim (~30 sec) plus this "manual" 3D Shim (another ~30 sec) is shorter than the approximately 90 secs it takes to do the Advanced shim. (See Note 3.) Thus, you can expect better results with this re-shim procedure compared to the simple "Invalidate All" approach that I gave in the last user training/FAQ. I'll write up a detailed explanation, along with results (field maps) showing the improved performance compared to the Standard shim, in the next version of the user training/FAQ.

Carry on!



1.  Some background information on distortion in the phase encoding axis is given in this post. An introduction to the acquisition and use of field maps to tackle distortion is included in my user training/FAQ document.

2.  No, that's not the monitor delivered with the scanner. Thanks for asking!! Some larger monitors will work perfectly well with the scanner and swapping for a larger one may be an option if you don't do clinical work and need to maintain that FDA approval thing. My scanner is pure research. If there's interest I'll post the specifications in a comment to this post. Also please note that the central GUI area cannot be enlarged, but you can use the black border around it to good effect with other windows. The various display programs can be run full screen, however. It's a really nice thing to have for teaching or to impress visitors.

3.  You can select a Standard or an Advanced shim on the product EPI sequences via the System tab, under Adjustments. It's the Shim mode parameter:

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