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--- b0_info [2014/10/01 17:00]
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-======EPI field map unwarping======
-This page contains information relevant to B0 field map un-warping, using the HUP6 (Siemens 3T) scanner and FSL FUGUE program.\\
-[[http://www.fmrib.ox.ac.uk/fsl/fugue/index.html|FSL_FUGUE]]
-=====Acquiring the b0 field map in the scanner=====
-The b0 field map acquisition is a Gradient Echo fieldmap sequence that takes ~64 seconds to run.
-  - 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.
-  - 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 {{:methods:b0map.pdf|protocol}} parameters with relevant fields highlighted. Mark Elliot can help you with this when you meet him to set up your scan protocol.
-  - Head coil does NOT matter. Use whichever you prefer.
-=====Processing the b0 field maps to your data=====
-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.
-  - 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 [[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide|here]].\\
-  - 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 {{http://cfn.upenn.edu/stslab/wiki_links/b0scripts/b0scripts.zip|here}}.
-    - 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.
-      - 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.'((Note that the above call uses BET brain extraction with a flag (-f 0.5) that manually sets the fractional intensity threshold for the brain extraction. The brain extraction is important, and must exclude all non-brain voxels and any voxels with only a small partial volume contribution. You should noodle around with the BET threshold until you are confident that this is the case.))
-      - 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.((This is because dcm2nii sets the 'scl_scope' to 2 in the header (for some reason?)... which is bad.)) So, **DO NOT use the -u flag** on the command line.
-    - 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.
-=====Applying the b0 field maps to your data using FSL=====
-  * If you intend to use a package other than FSL to process your data and run your analyses, then you may want to use [[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide|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 [[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide|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 {{:methods:b0map.pdf|scan protocol}}((**The values in this protocol are NOT necessarily the same as your actual scan protocol**. Please find a copy of your protocol at HUP6.)). (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\\

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