Functional-Sequences

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[edit] Overview

For many years we have used functional pulse sequences provided by the Radiology team at the Lucas Center. The emphasis there has been on spiral acquisitions, developed in the Macovski group and then expanded and maintained by Glover and his team. This differs from the much more widely used EPI methods, having some advantages and some disadvantages.

We have also explored new pulse sequence methods with the Pauly and Glover groups that are based on steady-state free precession methods. These are only in the early stages of development.

[edit] Pulse sequences

[edit] Gradient echo with spiral acquisition

For GRE BOLD methods, you'll want to adjust the flip-angle to optimize the SNR by maximizing the magnetization recovery along the z-axis (T1) during successive excitations of the same tissue (the repetition time- TR). The optimal flip-angle is found by the Ernst equation:

flip-angle = acos(exp(-TR/T1)) 
  • A typical T1 value for gray matter is (3T): 1.33 seconds (Kruger, et al, 2001).
  • At 1.5T, it is closer to 0.9 seconds.

If you need to know your optimal flip angle for any arbitrary TR, here's a calculator.

  • Or use the following values for typical TRs at 3T:
    • 3s > 84deg;
    • 2.5s > 81deg;
    • 2s > 77deg;
    • 1.5s > 71deg

[edit] Checking your image quality at the scanner (for spirals)

When scanning at the lucas center with Gary Glover's spiral sequence, the data are not reconstructed by the standard GE recon pipeline, so the images do not appear in the little image preview window. To see one of your images to check the data quality, you can use a couple of simple command-line tools. (Click the 'tools' icon and then open a C-shell.)

After the P.mag file has been created, open a C-shell and run:

cd /usr/g/mrraw
expandonefile -f 1 Pxxxx.7.mag filename nslc nframes npix
mdisp filename.*

Arguments for expanonefile:

  • xxxx: Pfile number
  • filename: output filename
  • nslc: number of slices
  • nframes: number of frames
  • npix: matrix size (next power of 2 >= frequency encode matrix; e.g., 64, 128 or 256)

Another tool is dodisp, which shows the first functional image in a run.

dodisp [run#]

e.g., for a file whose P-file is P01024.7, you would type dodisp 01024 or <code dodisp 1024 </code>.

Some notes from Gary on dodisp:

The resulting display will show all the slices in a montage. You can window/level with the center mouse button if the cursor is in the window, and quit in the usual window fashion, or by typing 'q' with the cursor in the window. This should be helpful in verifying the quality of your data. You can invoke it when the .mag file is complete. This is true when the "Writing_Pfile" file is gone from /usr/g/mrraw.

[edit] SSFP

We are working with Thomas John in Pauly group to develop bandpass SSFP for fMRI applications. This steady-state free precession (SSFP) method has the advantage that there is no image distortion. At present, however, the SNR of the method is inferior to conventional (GRE) methods.

We wrote an article Full-Brain Coverage and High-Resolution Imaging Capabilities of Passband b-SSFP fMRI at 3T. We are still not using the method regularly because of the low SNR. We are working on it.

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