Dear Mark,
Thank you very much for your reply.
I've talked to our physicist, and he says the value for the dwell time in
the DICOM field should be the correct one. I've also found a program at
UCSD's fmri center to unwarp EPI volumes called "ppge2", and this programs
searches for the same DICOM header field to get the dwell time. Moreover,
according to their website, they are also using a GE Excite 3.0T scanner,
and thus presumably the same software.
I am judging that the unwarping is to strong by looking, for example, at the
curvature of midline of the brain in an axial view in the volumes that have
the phase direction from left to right because the field is changing
relatively slowly in the center of the brain. Another place where it becomes
obvious is by looking at the position of the cerebellum in the saggital view
of the volumes where the phase directions is anterior-posterior, but there
are many places it can be seen, particularly in the moving GIFs from the
html report. I don't pay too much attention to the regions with drop-out, as
they can't be really restored anyhow.
The actual dwell time is 552 microseconds, and I've tried 552, 460, 368, 276
and 184 microseconds, both with and without using BET, and for volumes with
the phase directions being AP or LR. I've uploaded the EPI distorted and
undistorted EPI volumes, the fieldmap and its magnitude, the fieldmap
magnitude maps being forward warped according to the field, and a
high-resolution MPRAGE of the subject. The six-digit reference number for
this upload session is 177941.
By the way, the field map used for unwarping the EPI volumes with phase
direction AP was aquired with the phase direction LR, but I have a different
data set where the phase direction for the fieldmap was also AP, and the
effect is the same (and the field maps are very similar).
I think that the best match can be found with half of the dwell time (276
microseconds), or perhaps 2/3 (368 us) of the actual dwell time.
I don't have any further details on the ramp sampling, but if you agree that
the unwarping effect is to strong, and there isn't a mistake on my part in
the way I am running FUGUE, the fMRI center will contact GE to double check
on the field values, and we'll run a test session with and without ramp
sampling, see if the DICOM field changes, and whether the geometric
distortion depends on the ramp sampling.
Thank you very much for your help.
Have a great weekend,
Valentin
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