Updates for multiband reconstruction

March 15th, 2017
March 15th, 2017

The CNI has recently introduced a new option for reconstructing SMS (aka, multiband or mux) scans. The default reconstruction method in the SMS reconstruction pipeline is currently 1D-GRAPPA (Blaimer M. et al. MRM 2013). Based on recent research and testing, we believe that the split-slice-GRAPPA (Cauley SF, et al. MRM 2014) reconstruction algorithm does a better job at unaliasing the simultaneously acquired slices, especially in cases where the calibration data are corrupted by subject motion. This more robust unaliasing will help reduce the chance of false correlations in fMRI scans by reducing signal leakage across aliased slices.

Another advantage of the split-slice GRAPPA method is that it is less dependent on the image contrast being consistent between the calibration data and the SMS data, therefore it allows more flexibility in choosing the best calibration scans. So, we have also introduced a new SMS calibration scan option – using a separate single-band scan as an external calibration for the target SMS scan. Most of you doing SMS are using internal calibration, i.e. the first few volumes integrated in the SMS scans are used as the calibration data. And a few of you are doing an external calibration that has the same SMS (mux) factor as the target scan. Compared to these calibration methods, the single-band external calibration has higher SNR in the calibration data and is less sensitive to subject motion during the calibration. Therefore we believe it is a more robust calibration method, and in combination with the split-slice-GRAPPA reconstruction method, is likely to produce better image quality for the SMS scans, especially when you have wiggly subjects.

Here is a compelling example of how the single-band calibration scan can reduce a particularly insidious artifact due to excessive eye motion during the calibration scans (this subject was instructed to intentionally move their eyes during the calibration scans). In these standard deviation maps of the BOLD timeseries, the aliased eye artifact is clearly visible in the 1D GRAPPA reconstruction (top). The split-slice GRAPPA reconstruction (middle) shows a reduced eye artifact in the white matter, but there is still significant aliasing of the eyes. This aliasing is substantially reduced or eliminated in the same data reconstructed using a single-band calibration scan with split-slice GRAPPA (bottom), even though that also had subject eye movement.


However, in cases where there is no excessive motion during the calibration, all the methods are quite comparable:


The CNI SMS data processing pipeline will by default keep using the original 1D-GRAPPA reconstruction method for continuity of ongoing studies. And if you have compliant subjects who remain still, ideally with eyes-closed during calibration, this method should be fine. However, if you think your subjects may move during calibration, then we recommend switching to split-slice GRAPPA for image reconstruction. And you may also consider adding a single-band calibration scan to your protocol. Any SMS scan that doesn’t have a separate calibration scan setup in the same scan session will also be reconstructed using the internal calibrations. In order to use the new methods, you need to do the following in your protocol:

To use the split-slice-GRAPPA reconstruction method, include the keyword “_ssg” at the end of each series description that you want to be reconstructed with split-slice-GRAPPA. Note that this also enables SENSE1 coil combination (Sotiropoulos et. al., MRM 2014).

To use the single-band calibration, you need to set up a separate scan with SMS (mux) factor = 1 (CV 22). Include the keyword “_sbref” in the series description. This single-band scan needs to have the same coverage as the multiband scan, i.e. the same FOV and matrix size but X times the prescribed number of slices, X being the SMS (mux) factor. You will need to increase TR (by a few seconds) in order to accommodate all the slices in one TR. You only need 4 or 5 phases for this scan. Because the TR will be longer, you can set the flip angle to 90 to optimize SNR.

For scans using the single-band calibration, the calibration volume is not included in the reconstructed images, i.e. the NIFTI files will only contain the SMS volumes. This information is also shown in the JSON file that now accompanies all SMS NIFTI files in NIMS. The JSON file contains a list of important parameters related to the scan and the reconstruction.

Please contact Hua or Bob if you have any questions and/or want help setting up these new SMS features in your protocol. Also, we owe thanks to the Wagner and Poldrack labs for help in testing these new methods.

Posted in: Data Acquisition, NIMS, SMS

One comment

  1. chrisgor says:

    MRIQC (http://mriqc.org) was instrumental in finding this problem. I have uploaded quality reports from our pilot run comparing 1D-GRAPPA, SS-GRAPPA and different calibration scans here: https://github.com/chrisfilo/slice_leakage


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