fBIRN B0 Correction Recommendations

The fBIRN will be correcting for distortion caused by B0 inhomogeneity in EPI scans by collecting a field map and applying the image-based dewarping tools from the FSL software package. This will only be applied to those scans acquired with a raster-style EPI k-space trajectory. Spiral EPIs will not be dewarped in this way.

We recommend using the following parameter set for the B0 mapping sequence.:

TR = 500ms (1000ms with phased-array).
TE1: Minimum possible
TE2 = TE1 + DeltaTE

DeltaTE = 4.92ms for 1.5T
Flip Angle: 65 for 1.5T
DeltaTE = 2.46ms for 3T
Flip Angle: 55 for 3T
DeltaTE = 1.845ms for 4T
Flip Angle: 55 for 4T

FatSat: Off
Bandwidth: Maximum
Slice Prescription, FOV, Thickness, Skip, Pixel Resolution, Matrix Size:
same as functional

The DeltaTE is set so that the water and fat re-phase and might differ slightly on individual systems from the values listed below depending upon the exact strength (eg, 2.89T instead of exactly 3T).

For Siemens, we recommend using the stock sequence called gre_field_mapping. Below are links to Siemens DICOM files for the field mapping sequences with the above parameters for the Avanto, Trio, and Allegra scanners. Siemens sites may be able to import these scans directly into the scanners using the Phoenix capability.
Siemens Avanto Field Map DICOM File
Siemens Trio Field Map DICOM File
Siemens Allegra Field Map DICOM File

After the data have been collected, the following script can be run to dewarp the EPI scans. There is EXTENSIVE documentation that can be obtained by running this scrip with the --help option. A link to this help page is also given below. Those in the MGH-NMR Center already have access to this script through the standard environment.
Dewarping Script (epidewarp.fsl)
Help Page for Dewarping Script (epidewarp.fsl --help)

Other references:
FSL Fugue Home Page
Helsinki University EPI Distortion Page
Thomas Benner's Protocol Page