Field-map undistortion v3.03 July 2004
Batch mode description
These are all now properties of a structure, so you set them using something like
bp.acceptalldefaults=1
When you run the tool using the GUI, it saves this structure to a file “parameters.mat” in the directory where you
store the field map intermediates (as specified in phasemapdirectory below, or entered as “field map directory” in
the GUI). You could use this as a basis for your batch script.
You may run the tool in batch mode by providing this structure as a parameter
e.g., fieldmap_undistort_v3(bp)
where bp is the structure you’ve made.
The Cambridge only options extract parameters from the Bruker files that will be unique to our site. However, with
a little modification they could be used where preprocessed fieldmaps are available in Analyze format.
COMMON TO ALL RECO IMPORT MODES
NAME
DESCRIPTION
POSSIBLE VALUES
acceptalldefaults
Whether to accept default values for
parameters below
startstage
Stage of processing to start at
recophasemaps
Where phase maps are/ will be
reconstructed
0 No
1 Yes
2 Use same parameters as last
time
0 Reco
1 Unwrapping
2 Skull stripping
3 Expansion
4 Rotation & reslicing
5 Generate distorted magnitude
6 Coregistration
7 Undistortion
1 Locally reconstructed
0 Reconstructed with WBIC tool
2 Varian field maps
3Bruker Queensland field maps
4 Siemens gre_fieldmapping
5 Separate Analyze format field
maps
6Ready preprocessed fieldmaps
in Tesla',...
evoltime
Difference in echo time of two maps
(ms)
phaseencodeaxis
Phase encode axis along which
undistortion will be applied
phasemapdirectory
epitocoreg
Directory for field map data files
Filename of EPI to coregister to
(usually mean*...)
Filename( s) of EPIs to undistort
Interpolation type
epistoundistort
interpol
2.276
9.104 (Cambridge default)
2.5
8.104
2.46 (Siemens GRE
fieldmapping default)
1–x
2–y
3–z
linear
WHEN
REQUIRED
Always
Always
Anything up to
stage 5
Anything up to
stage 5
Always
Always
Anything up to
stage 6
Always
Always
realigntocom
manualshift
padz
zerodisp
maxshift
constrain
Whether to realign field maps to their
centre of mass at start of processing
Shift EPI forward by this many mm
during undistortion process (very
occasionally necessary to keep them
within field of view)
Pad fieldmap above and below in z
dirextion by this many voxels
Adjust undistortion map so mean
displacement is zero (helps to keep
everything in FOV)
Mask voxels that shift by more than
this distance in mm
Constrain coregistration of EPI and
distorted field map magnitude to only
allow translations
sinc (default)
0 No
1 Yes (default)
defaults to zero
0 No
1 Yes
Anything up to
stage 4
Anything up to
stage 5
defaults to 9999
Always
0 No
1 Constrain to translations only
(default)
Anything up to
stage 6
SIEMENS GRE_FIELDMAPPING SEQUENCE
gre_phase
gre_fieldmapping Analyze format
phase
gre_mag
gre_fieldmapping Analyze format
magnitude
Anything
before stage 5
Anything
before stage 5
ANALYZE FORMAT FIELDMAPS
fmA_m
Magnitude of fieldmap A
fmA_p
Phase of fieldmap A
fmB_m
Magnitude of fieldmap B
fmB_p
Phase of fieldmap B
Anything up to
stage 5
Always
Anything
before stage 5
Anything
before stage 5
Anything
before stage 5
Anything
before stage 5
CAMBRIDGE ONLY: OLD FIELDMAPS
phasemappair
(bandwidth)
phasemapdirectory
phase1a
phase1b
phase1c
phasecmr
Whether to use phase 1a and 1b or
phase 1a and 1c
No longer required – extracted
automatically from imnd or .brkhdr file
Directory for data files
Directory of phase1a data (if
reconstructing locally)
Directory of phase1a data (if
reconstructing locally)
Directory of phase1a data (if
reconstructing locally)
Filename of .cmr file (if
reconstructing at WBIC)
1 1a and 1b maps
2 1a and 1c maps
Always
Never
Always
Anything
before stage 5
Anything
before stage 5
Anything
before stage 5
Anything
before stage 5
CAMBRIDGE ONLY: NEW FIELDMAPS, PRE-PROCESSED AND SCALED IN TESLA
newfieldmap
Path to directory containing Analyze
Anything
format files:
before stage 5
magnitude.img
fieldmap.img
matfile.txt 4x3 rotation/translation
matrix (use [1 0 0 0; 0 1 0 0; 0 0 1 0] if
no rotation or translation needed)
OXFORD ONLY
oxmap
Filename of _b0map file
procpar
Filename of EPI procpar file
Anything
before stage 5
Anything
before stage 5