||<100% bgcolor="#FFFF99">'''Using a field-map to undistort EPIs'''<<BR>>[[FmBackground|Background]]<<BR>>[[FmPower|Improvement in power!]]<<BR>>[[FmFieldmaps|Acquiring fieldmaps]]<<BR>>[[FmDownload|Download]]<<BR>>[[FmRequirements|What you'll need to undistort an EPI data series]]<<BR>>[[FmReference|Guide and reference]]<<BR>>[[FmExample|Step-by-step example]]<<BR>>[[FmBatch|Batch mode]]||

== Siemens step-by-step example ==
First, get the [[http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_siemens_exampledataset.tar|Siemens example dataset (2MB)]] (thanks to Michael Benharrosh and Marlene Richter at Princeton University for this).

Unzip it and you should have three images in analyze format: an EPI, and the phase and magnitude from a gre_fieldmapping sequence.

When you've installed the tool, at the matlab prompt type

>> fieldmap_undistort_v3

Then, in the SPM window, choose the following options

||<tablewidth="90%">Accept all defaults||No||
||Start at which stage||Reco ''(default)''||
||Which option?||Siemens gre_fieldmapping||
||Realign fieldmaps to com||Yes ''(default)''||
||Shift EPI forward by||0 ''(default)''||
||Evolution time||2.46 ''(default)''||
||Slice angle of EPIs relative to fieldmaps||0 ''(default)''||
||Bandwidth||2604||
||Axis of phase encoding (undistortion)||y ''(default)''||
||Constrain coregistration||Translations only ''(default)''||
||Type of interpolation||sinc ''(default)''||
||Maximum shift allowed||9999 ''(default)''||
||Adjust mean displacement?||Force mean to zero ''(default)''||
||Directory for fieldmap files||Choose a blank directory (e.g., fieldmaps)||
||Choose GRE phase map||PHANTOM_FIELDMAP_PHASE.img||
||Choose GRE magnitude map||PHANTOM_FIELDMAP_MAG.img||
||Choose EPI to coregister to||PHANTOM_EPI.img||
||Choose EPIs to undistort||PHANTOM_EPI.img||
The EPI before and after undistortion should look like this:

||<tablewidth="90%"> {{http://imaging.mrc-cbu.cam.ac.uk/images/fm_phantom_before_undist.jpg}} || {{http://imaging.mrc-cbu.cam.ac.uk/images/fm_phantom_after_undist.jpg}} ||
There's nothing that can be done about the dropout, but even the large distortion produced by this mis-shimming is mostly corrected.

If you are going to collect your own data on a Siemens machine and your system doesn't allow you to reconstruct both mag and phase simultaneously, you'll need to change one line in your pulse sequence. Contact Stefan Thesen at Siemens [his surname] @siemens.com who'll probably be able to help.)

== Bruker step-by-step example ==
First, get the [[http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_exampledataset.tar|Bruker example dataset (34MB)]]

Run by typing fieldmap_undistort at the SPM prompt, and choose the following options. Where requested, choose the directories and files from your copy of the data.

||<tablewidth="638px"^ 38%>Accept all defaults: ||<^ 62%>Yes ||
||<^ 38%>Choose Directory of Phase Map: ||<^ 62%>example_dataset/phasemaps ||
||<^ 38%>Choose Directory of Phase 1a: ||<^ 62%>example_dataset/rawprereco/10 ||
||<^ 38%>Choose Directory of Phase 1b: ||<^ 62%>example_dataset/rawprereco/11 ||
||<^ 38%>Choose Directory of Phase 1c: ||<^ 62%>example_dataset/rawprereco/12 ||
||<^ 38%>Choose EPI header file (IMND or brkhdr): ||<^ 62%>example_dataset/epis/000484 m03_04_EPI.brkhdr ||
||<^ 38%>Choose EPI to register to: ||<^ 62%>example_dataset/epis/meany000484-m03_04_EPI_0002.img ||
||<^ 38%>Choose EPI to undistort: ||<^ 62%>example_dataset/epis/meany000484-m03_04_EPI_0002.img ||
The undistorted EPIs will be in the same directory as the raw EPIs, with the added suffix ‘u’.