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||<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]|| | ||<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] || == 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). |
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== Download == === What software you'll need === Matlab |
Unzip it and you should have three images in analyze format: an EPI, and the phase and magnitude from a gre_fieldmapping sequence. |
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SPM 99 or above | When you've installed the tool, at the matlab prompt type |
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If you are using Bruker format input files, a Perl interpreter (e.g, from cygwin.com) | >> fieldmap_undistort_v3 |
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If you wish to compile the code, you'll need Perl and gcc or cxx, or a love of the joy of programming. | Then, in the SPM window, choose the following options |
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=== What data you'll need === Field maps (see 'Acquiring fieldmaps' above) |
||<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: |
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Echo planar functional data in Analyze format | ||<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. |
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=== Licensing === If you are an academic user you may download this software for free immediately: please first download a license form. [http://imaging.mrc-cbu.cam.ac.uk/text/undistortion_licence.doc Download this one] if you are downloading the compiled version, or [http://imaging.mrc-cbu.cam.ac.uk/text/undistortion_source_licence.doc this one] if you are downloading the source code. Before you download the software, please sign and return two copies of the appropriate form. |
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.) |
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If you are a commercial user please email rhodri.cusack@mrc.cbu.cam.ac.uk | == Bruker step-by-step example == First, get the [http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_exampledataset.tar Bruker example dataset (34MB)] |
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=== Download version 3.03 === [http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_siemenes_exampledataset.tar Siemens example dataset (2MB)] |
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. |
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[http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_exampledataset.tar Bruker Example dataset (111MB)] [http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_v3p03_solaris.tar Sun (solaris) (4MB)] [http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_v3p03_linux.tar Linux (Red Hat) (4MB)] [http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_v3p03_windows.tar Windows (4MB)] [http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_v3p03_withsrc.tar Source code (all platforms, requires Perl, and either GCC or MS Visual Studio or CXX) (17MB)] |
||<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’. |
||<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] ||
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’.