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