Print

---

Hi John

I can run the FieldMap now. But there are some problems still. The
parameters which I used are as follow:

I used MATLAB2006 FieldMap2.0 and SPM5. I used the fieldmap to correct the
distortion of EPI scan. The data which I used is the FieldMapExampleData of
FieldMap. I did follow manual. I used the nepi_stretch in FieldMaExampleData
as the data. I revised the parameters in the file PM_default.m as follow:



% SPM5 UPDATE 16/12/06

% UPDATE 27/01/05

% Sets the default values for the FieldMap toolbox

%

% FORMAT pm_defaults

%_______________________________________________________________________

%

% This file is intended for site and/or scanner and/or

% sequence-specific customisations.

%_______________________________________________________________________

% pm_defaults Chloe Hutton, Jesper Andersson 17/12/06



global pm_def



% Defaults for creating field map. (See pm_make_fieldmap.m and

%                                   FieldMap.man for more info.)

%=======================================================================

pm_def.INPUT_DATA_FORMAT = 'PM';      % 'RI' = load two real and

                                      % imaginary image pairs

                                      % 'PM' = load one or two

                                      % phase and magnitude image

                                      % pairs.

pm_def.SHORT_ECHO_TIME = 10.0;        % Short echo time in ms for Allegra

pm_def.LONG_ECHO_TIME = 14.76;%12.46;        % Long echo time in ms for
Allegra

pm_def.MASKBRAIN = 0;                 % Do brain masking (1 or 0,

                      % 0 for EPI fieldmaps)



% Defaults for unwrapping options. (See pm_make_fieldmap.m and

%                                   FieldMap.man for more info.)

%=======================================================================

pm_def.UNWRAPPING_METHOD = 'Mark3D';  % Unwrapping options are:

                                      % 'Huttonish', 'Mark3D' or 'Mark2D'

pm_def.FWHM = 10;                     % FWHM of Gaussian filter used to

                                      % implement weighted smoothing of

                                      % unwrapped maps.

pm_def.PAD = 0;                       % Size of padding kernel if required.

pm_def.WS = 1;                        % Weighted or normal smoothing.



% Flags for brain extraction

%=======================================================================

% Default T1 template for segmentation

pm_def.MFLAGS.TEMPLATE = fullfile(spm('Dir'),'templates','T1.nii');

pm_def.MFLAGS.FWHM = 5; % In mm - used for smoothing to fill holes in brain
mask

pm_def.MFLAGS.NERODE = 1;% In voxels - used for erosion to remove scalp from
brain mask

pm_def.MFLAGS.NDILATE = 2; % In voxels - used for dilaton to condition scalp
removal

pm_def.MFLAGS.THRESH = 0.5; % Intensity thresholding for filling holes

pm_def.MFLAGS.REG = 0.02; % A larger value helps segmentation to converge

pm_def.MFLAGS.GRAPHICS = 0; % Don't display segmentation results



% Defaults for converting field map to voxel displacement map.

%=======================================================================

pm_def.EPI_BASED_FIELDMAPS = 0;        % EPI=1, other=0.

pm_def.K_SPACE_TRAVERSAL_BLIP_DIR = 1;%-1; % +ve k-space = 1, -ve = -1.

pm_def.TOTAL_EPI_READOUT_TIME = 32;%21.1;    % Allegra EPI RO time
(330E-6*64)



% Defaults for Unwarping.

%=======================================================================

pm_def.DO_JACOBIAN_MODULATION = 0;    % Do jacobian modulation to adjust

                                      % for compression or stretching

                                      % No = 0, Yes = 1





return;



But the results field map sheared after I did "MatchVDM to EPI", or I load
structural (if I did not do "MatchVDM to EPI". How can I solve this problem?
Thank you.

Sincerely

Wang Qiang