Hi
We also collect fieldmap series from a Siemens 3T and have successfully used
Jesper Anderson and Chloe Hutton's fieldmap toolbox to undistort EPI images.
It works well and is simple to use. Here are a few pointers and steps to
getting the toolbox going:
1) convert the phase series to radians - Chloe earlier emailed the list with
this function:
function pm_phase2rad
% Script to scale a phase map so that max = pi and min =-pi radians.
% Writes out scaled image prepended with 'sc'.
% spm_defaults
V=spm_vol(spm_get(1,'*.img','Select phase'));
vol=spm_read_vols(V);
mn=min(vol(:));
mx=max(vol(:));
svol=-pi+(vol-mn)*2*pi/(mx-mn);
oV=V;
name='sc';
oV.fname=[spm_str_manip(V.fname, 'h'), ...
[filesep name deblank(spm_str_manip(V.fname,'t'))] ];
oV.dim(4)=spm_type('double');
spm_write_vol(oV,svol);
2) change the input data format to phase/magnitude in pm_defaults.m
[line 18] pm_def.INPUT_DATA_FORMAT = 'PM'
3) although not necessary, it's helpful to set the short/long ehco times at
lines 23-24.
4) remember that you only select one magnitude and one phase image - the
Siemens fieldmapping sequence creates a "subtracted" phase image.
Cheers,
Paul
On Wed, 8 Jun 2005 23:04:12 -0400, Geoffrey K Aguirre
<[log in to unmask]> wrote:
>Hello --
>
> I'm trying to perform distortion correction on EPI data
>collected on a 3T Siemens scanner. I have installed the CBU software
>and have it working with the sample "Siemens" phantom data. However,
>my attempts to apply the method to my data have been unsuccessful. My
>magnitude and phase images seem to have the same properties (e.g.,
>range of values) as the files in the sample data, but when I perform
>the correction it munges my EPI from this:
> to this
>.
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