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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]
||
== Download ==
=== What software you'll need ===
Matlab		 ||<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]]||
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SPM 99 or above == 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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If you are using Bruker format input files, a Perl interpreter (e.g, from cygwin.com) 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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If you wish to compile the code, you'll need Perl and gcc or cxx, or a love of the joy of programming. When you've installed the tool, at the matlab prompt type
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=== What data you'll need ===
Field maps (see 'Acquiring fieldmaps' above)		 >> fieldmap_undistort_v3
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Echo planar functional data in Analyze format Then, in the SPM window, choose the following options
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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.		 ||<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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If you are a commercial user please email rhodri.cusack@mrc.cbu.cam.ac.uk ||<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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=== Download version 3.03 ===
[http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_siemenes_exampledataset.tar Siemens example dataset (2MB)]		 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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[http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_exampledataset.tar Bruker Example dataset (111MB)] == 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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[http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_v3p03_solaris.tar Sun (solaris) (4MB)] 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_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’.

Using a field-map to undistort EPIs
Background
Improvement in power!
Acquiring fieldmaps
Download
What you'll need to undistort an EPI data series
Guide and reference
Step-by-step example
Batch mode

Siemens step-by-step example

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 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 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’.

CbuImaging: FmExample (last edited 2013-03-07 21:24:05 by localhost)