82013-03-07 21:24:05localhostconverted to 1.6 markup72006-07-27 14:53:14devel01.mrc-cbu.cam.ac.uk62006-07-27 14:52:56devel01.mrc-cbu.cam.ac.ukRevert to revision 3.52006-07-27 14:50:56devel01.mrc-cbu.cam.ac.uk42006-07-27 14:22:32devel01.mrc-cbu.cam.ac.uk32006-07-27 10:03:07devel01.mrc-cbu.cam.ac.uk22006-07-27 10:01:42devel01.mrc-cbu.cam.ac.uk12006-07-04 15:01:25Scripting SubsystemUsing a field-map to undistort EPIsBackgroundImprovement in power!Acquiring fieldmapsDownloadWhat you'll need to undistort an EPI data seriesGuide and referenceStep-by-step exampleBatch mode

First, get the 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 Accept all defaultsNoStart at which stageReco (default)Which option?Siemens gre_fieldmappingRealign fieldmaps to comYes (default)Shift EPI forward by0 (default)Evolution time2.46 (default)Slice angle of EPIs relative to fieldmaps0 (default)Bandwidth2604Axis of phase encoding (undistortion)y (default)Constrain coregistrationTranslations only (default)Type of interpolationsinc (default)Maximum shift allowed9999 (default)Adjust mean displacement?Force mean to zero (default)Directory for fieldmap filesChoose a blank directory (e.g., fieldmaps)Choose GRE phase mapPHANTOM_FIELDMAP_PHASE.imgChoose GRE magnitude mapPHANTOM_FIELDMAP_MAG.imgChoose EPI to coregister toPHANTOM_EPI.imgChoose EPIs to undistortPHANTOM_EPI.imgThe EPI before and after undistortion should look like this: 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.)

First, get the 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. Accept all defaults: Yes Choose Directory of Phase Map: example_dataset/phasemaps Choose Directory of Phase 1a: example_dataset/rawprereco/10 Choose Directory of Phase 1b: example_dataset/rawprereco/11 Choose Directory of Phase 1c: example_dataset/rawprereco/12 Choose EPI header file (IMND or brkhdr): example_dataset/epis/000484 m03_04_EPI.brkhdr Choose EPI to register to: example_dataset/epis/meany000484-m03_04_EPI_0002.img Choose EPI to undistort: 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’.