When I run the command line version of Eddy Correct the output is a 3D
volume instead of a 4D volume. However, running Eddy Correct using the same
data set worked normally using the GUI method. Looking at the log file, the
command line version runs one extra volume (volume.hdr) at the end and
apparently just outputs this volume - I am not sure why. Is there something
I am doing wrong with the command line utility? The actual command was:
eddy_correct Diffusion_4D.nii Diffusion_Eddy 0
Examples of the log files for the two versions are below:
----------------------------------
End of the log file - GUI version
----------------------------------
processing vol0064.nii.gz
Final result:
1.013938 0.005867 0.003907 -2.351779
0.002403 1.018577 0.021935 -1.948520
-0.000394 -0.005939 1.032645 -0.812195
0.000000 0.000000 0.000000 1.000000
-------------------------------------
--------------------------------------
End of log file - command line version
--------------------------------------
processing vol0064.nii.gz
Final result:
1.013938 0.005867 0.003907 -2.351779
0.002403 1.018577 0.021935 -1.948520
-0.000394 -0.005939 1.032645 -0.812195
0.000000 0.000000 0.000000 1.000000
processing volume.hdr
Final result:
1.006663 0.149024 -0.046140 135.947793
-0.177441 1.031282 0.036865 -105.707561
0.061827 -0.017788 1.050493 -3540.717876
0.000000 0.000000 0.000000 1.000000
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