Hi Daniel - It'll be easier to just preprocess the data before passing them to
trac-all. Topup will be incorporated to the preprocessing for the next version
release. Of course you can replace that part of the script yourself if you
prefer - you'll have to also combine the AP and PA outputs etc etc.
Best,
a.y
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow
<ddcc2...@gmail.com>
Sent: Tuesday, July 30, 2019 8:44:32 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA incorporate topup instead of field map?
External Email - Use Caution
Hello,
I have previously used field map correction for b0 inhomogeneities when running
TRACULA, however my new data set has A>P and P>A encoding. I know that topup
has been shown to perform slightly better than filed map correction. I wonder
if it would be possible to manually edit the
($dob0) then # B0-inhomogeneity "correction"
part of the code and run topup instead of epidewarp.fsl? I am trying to
determine how feasible this is and was wondering if this had been tried by
others?
If not, does it make more sense to process the data with topup separately and
then incorporate it into TRACULA?
Thank you for any guidance you can provide,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
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