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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] || == 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). |
||<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]|| |
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| Unzip it and you should have three images in analyze format: an EPI, and the phase and magnitude from a gre_fieldmapping sequence. | == Download == === What software you'll need === Matlab |
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| When you've installed the tool, at the matlab prompt type | SPM 99 or above |
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| >> fieldmap_undistort_v3 | If you are using Bruker format input files, a Perl interpreter (e.g, from cygwin.com) |
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| Then, in the SPM window, choose the following options | If you wish to compile the code, you'll need Perl and gcc or cxx, or a love of the joy of programming. |
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| ||<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: |
=== What data you'll need === Field maps (see 'Acquiring fieldmaps' above) |
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| ||<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. |
Echo planar functional data in Analyze format |
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| 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.) | === 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. |
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| == Bruker step-by-step example == First, get the [http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_exampledataset.tar Bruker example dataset (34MB)] |
If you are a commercial user please email rhodri.cusack@mrc.cbu.cam.ac.uk |
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| 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. | === Download version 3.03 === [http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_siemenes_exampledataset.tar Siemens example dataset (2MB)] |
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| ||<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’. |
[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)] |
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] |
Download
What software you'll need
Matlab
SPM 99 or above
If you are using Bruker format input files, a Perl interpreter (e.g, from cygwin.com)
If you wish to compile the code, you'll need Perl and gcc or cxx, or a love of the joy of programming.
What data you'll need
Field maps (see 'Acquiring fieldmaps' above)
Echo planar functional data in Analyze format
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 a commercial user please email rhodri.cusack@mrc.cbu.cam.ac.uk
Download version 3.03
[http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_siemenes_exampledataset.tar Siemens example dataset (2MB)]
[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)]