FmExample - MRC CBU Imaging Wiki

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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).

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 ā€˜uā€™.