Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [lostrow...@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space Hi Anastasia, I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from? Lauren ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space 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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [lostrow...@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
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