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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow <ddcc2442@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

ddcc2442@gmail.com

443-254-6298

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