This page contains information relevant to B0 field map un-warping, using the HUP6 (Siemens 3T) scanner and FSL FUGUE program.
FSL_FUGUE

The b0 field map acquisition is a Gradient Echo fieldmap sequence that takes ~64 seconds to run.

1. Add the b0 field map sequence to your protocol by contacting Mark Elliot (melliott@mail.med.upenn.edu) and setting up a time to meet with him at the scanner to set up your scan protocol. Since I do not know the parameters of your scan sequence, I do not want to point you toward a sequence that may be incorrect for your protocol.
2. After the sequence has been added to your protocol, make sure that these parameters match: (number of) slices, slice thickness, field of view (FoV), and shim mode. All of these can be found on the “Routine” page of the sequence parameters, except for shim mode. Shim mode can be found on the “System” page of the sequence parameters. It should either read “standard” or “advanced”. Most protocols are set to “standard”, but this b0 map sequence is set to “advanced”- It does not need to be. Just make sure that all of the epi runs' shim mode matches the b0 shim mode. Here is an example of the scanner protocol parameters with relevant fields highlighted. Mark Elliot can help you with this when you meet him to set up your scan protocol.
3. Head coil does NOT matter. Use whichever you prefer.

Once you have uploaded your scan data and sorted the raw dicoms into runs, you will see that you have 2 b0 map directories: One is a magnitude image and the other is the phase image.

1. If you have used the gre_field_map (siemens stock) sequence to acquire your b0 maps (this is most likely the case), then all you need to know can be found here.
   
2. If you used a custom sequence that was created by Mark Elliot, then you will need to use a special pipeline to process the b0 maps before you feed them into fsl's fugue. Download the scripts for this pipeline here.
   1. Please read the information in the main call script, 'dico_b0calc_v2.sh.' for information on how to call the script from the command line, and which flags you will want to use.
      1. An example of command line usage is:
         sh $dir/dico_b0calc_v2.sh -mxFs -f 0.5 outfile_root magnitude_dicom_folder/* phase_dicom_folder/*
         Find flag usage information in the header of 'dico_b0calc_v2.sh.'¹⁾
      2. When using the above script, be sure not to use dcm2nii to create your nifti images. When converting the phase dicoms to nifti using dcm2nii, the pixels values are twice what they are when using t03d to convert the phase dicoms.²⁾ So, DO NOT use the -u flag on the command line.
   2. This pipeline will output some files. The most important of which are: 'mag1' and mag1_brain', and 'rpsmap.' Keep these in the same directory. The mag1_brain will be used as the magnitude image and the rpsmap will be used as the phase image in FSL FUGUE.

• If you intend to use a package other than FSL to process your data and run your analyses, then you may want to use FUGUE to unwarp your epi images before pre-processing.
  
• If, on the other hand, you intend to use FSL for all phases of your data handling, then you should use FEAT to unwarp the epi images.
  

The fsl wiki contains very clear documentation on how to use FEAT & FUGUE. Please read the information there before proceeding with the b0 field map unwarping.

• When unwarping the epi runs in FSL (feat or fugue), you will need to know the echo time and echo spacing for your epi runs. Find these in the scan protocol³⁾. (echo time = 'TE', and is found under the 'routine section of the protocol. Echo spacing can be found under the 'sequence' section of the protocol.

Need further assistance? apersi@sas.upenn.edu