Diff for "FmExample" - MRC CBU Imaging Wiki
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== Download ==
=== What software you'll need ===
Matlab
== 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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SPM 99 or above 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 are using Bruker format input files, a Perl interpreter (e.g, from cygwin.com) When you've installed the tool, at the matlab prompt type
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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. >> fieldmap_undistort_v3
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=== What data you'll need ===
Field maps (see 'Acquiring fieldmaps' above)
Then, in the SPM window, choose the following options
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Echo planar functional data in Analyze format ||<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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=== 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%"> 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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If you are a commercial user please email rhodri.cusack@mrc.cbu.cam.ac.uk 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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=== Download version 3.03 ===
[http://imaging.mrc-cbu.cam.ac.uk/downloads/fmu/fmu_siemenes_exampledataset.tar Siemens example dataset (2MB)]
== 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_exampledataset.tar Bruker Example dataset (111MB)] 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_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’.

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