Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a
bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc
script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu]
Sent: Tuesday, May 30, 2017 1:46 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration
manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject
registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be
happening and how to correct it?
Thanks,
Lauren Ostrowski