Thank you, Michael!
Do you know for this section:
# "Effective" Echo Spacing of *Spin Echo Field Maps*. Specified in
seconds.
# Set to "NONE" if not used.
# SEEchoSpacing = 1/(BWPPPE * ReconMatrixPE)
# where BWPPPE is the "BandwidthPerPixelPhaseEncode" = DICOM field
(0019,1028) for Siemens, and
# ReconMatrixPE = size of the reconstructed SEFM images in the PE
dimension
# In-plane acceleration, phase oversampling, phase resolution, phase
field-of-view, and interpolation
# all potentially need to be accounted for (which they are in Siemen's
reported BWPPPE)
#
# Example value for when using Spin Echo Field Maps from the
HCP-YA
# 0.000580002668012
SEEchoSpacing="NONE"
How I would know what the appropriate value of **SEEchoSpacing** would
be for my data?
Also, is it safe to assume:
TopUpConfig="${HCPPIPEDIR_Config}/b02b0.cnf”. ?
Thanks again!
On 18 Jul 2018, at 0:20, Harms, Michael wrote:
Hi,
If you are using SEFMs, you don't need to generate magnitude and phase
field maps. It is handled internally. See the Batch script in the
Examples directory.
Cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
On 7/17/18, 11:12 PM, "hcp-users-boun...@humanconnectome.org on
behalf of Marc Dubin" <hcp-users-boun...@humanconnectome.org on behalf
of mrd9...@med.cornell.edu> wrote:
Dear All,
I am new to the HCP MR pipelines and was wondering if anyone can
provide
guidance on how to generate magnitude and phase field maps for input
to
PreFreeSurferPipelineBatch.sh
The files that I currently have from the Siemens 3T scanner are:
SpinEchoFieldMap_PA
SpinEchoFieldMap_AP
Thanks for any suggestions!!
Marc Dubin
Marc Dubin, MD PhD
Assistant Professor of Psychiatry and Neuroscience
Department of Psychiatry and Brain and Mind Research Institute
Weill Cornell Medicine | New York-Presbyterian
Psychiatry-Box 140
525 East 68th Street
New York, NY 10065
T 212.746.5817
mrd9...@med.cornell.edu
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