Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.

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 7:55 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space

Hi Anastasia,

It looks as though some but now all have updated -

[franklin:xfms] (nmr-dev-env) ls -l

total 152

-rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat

-rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~

-rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat

-rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat

-rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat

-rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat

-rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat

-rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~

-rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log

-rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old

-rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost

-rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param

-rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum

-rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat

-rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat

-rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat

-rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat

-rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat

-rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat

-rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat

-rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat

Thanks,

Lauren

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu]
Sent: Tuesday, May 30, 2017 6:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space

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-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 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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@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-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