Hi Ela - Just confirming that my suggestion was to try to increase the degrees
of freedom with bbregister, if you see the kind of effect that you were
describing (where the registration is better in one part of the brain than
another, likely because of uncorrected distortions between DWI and T1).
Anastasia.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Salar Dini, Elaheh
<elaheh.salard...@yale.edu>
Sent: Monday, January 10, 2022 4:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Trac-all -prep -c error
External Email - Use Caution
Thank you for constantly improving TRACULA. I believe we don't have reverse
polarity scan or a field-map. We might be able to acquire the field-map though
since the MRI has been acquired locally.
Having that in mind, and just for clarification and making sure I have
understood you correctly, do you still propose to choose bbregister for
intera-subject, nonlinear FA-to-FA with SyN for inter-subject and intradof=12?
Or do you propose to try both bbregister and Flirt for intra-subject
registration in addition to trying different intradof ?
I would love to run both bbregister and Flirt and compare the results between
the two methods, but I believe we can't run Flirt because the
trctrain/hcp/mgh_10xx/mni folder, doesn't contain acomm.flt.prep.trk file; This
folder, however, has the acomm.bbr.prep.trk in it. I believe that is why we can
run trac-all -prep without an error setting the registration method as
bbregister but we get error when we change it to Flirt. This is at least true
for the freesurfer 7.2.0 that we installed on our server using
freesurfer-linux-centos7_x86_64-7.2.0.tar.gz package.
My best wishesm
Ela
From: Yendiki,
Anastasia<https://secure-web.cisco.com/1knn_2pxPUKVzJMh8_dhNql71BhVr-w9uwEiMOa5zQ0QQEz_OCLzXiP1vJU76vn0CD0TnILCseJTwgNUnbvBJx5M2WK8faHML9otyZK0rq_CN86mxx5jy-yCHMFGQ-WRiJX5UXcWDYTArEGX3_BE54h-UiOX0mrjwp2cEb2TaUMIydn0RHb9_Bmrxn-FUyJVc_BuCchoY88gjYZyofPtAe1gjgJZMbGzclo_kfJ2FrD1OwFpj6jh5ysfieFTcRC4Vz91J8Z3EM4j2e07RmJ9mnKSq4zHxbOvPmrwSu7Ahb6hj7_qIgKdAJCR1LHxq20rY8p89xERpx9rOp0BZFe7RMQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Yendiki%252C%2BAnastasia%2522>
Sent: Sun, 09 Jan 2022 19:06:53
-0800<https://secure-web.cisco.com/1LbPUjKqPGJSL_N-GoC6h2T-dPkw_3MYP55OUQOttI1HVbvgiGAdF67MIERFzfOjWJXpn58VbIcA32gmsmDXmPaucc0xpoMckesxJoZtRpNAw2WMUGdJAi6uxurFHhxpiDWjMJVmF0zGpSdsg72u2z_kU1VPKPPJWVQLUt_nsIgmUnP7z4wWqVNpk3oxkz_JEdgsMgVgsLS8Ytv8fzI35ztfhfR7aU_BFnQPfhc9GMrpzqNM8bY7B8Hz3-P6RAEqAdzXxDFh-x9mfP-wXq5WcEouezgwBs2A838QNOgStBsIW8lrV_ODVe6vBMpUQ_rqRa7DHalTIUMXKWJt5X93Rqg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220109>
To: elaheh.salard...@yale.edu
Subject: Re: Trac-all -prep -c error
Interesting! I had not observed that, but I was not specifically looking for
it. I imagine that this may vary depending on how much EPI distortion there is
in the diffusion data to being with, if a field map or reverse polarity scan is
used to correct this distortion, etc.
In the new version, there is an option to set the degrees of freedom for the
affine inter-subject registration, in your config file. (This should work
either with bbregister or with flirt.)
For example, this gives you rigid registration (rotation + translation only):
set intradof = 6
This gives you rigid + scaling:
set intradof = 9
This gives you full affine:
set intradof = 12
Depending on how much distortion there is in your diffusion data, increasing
the DoF in the registration to the T1 may give you better results. I'd actually
be very interested in hearing what worked best for you.
Thanks to you and your instructor for bringing this to our attention!
Anastasia.
________________________________
From: Salar Dini, Elaheh <elaheh.salard...@yale.edu>
Sent: Sunday, January 9, 2022 8:26 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: Trac-all -prep -c error
Dear Anastasia,
I just wanted to share with you that after following up with our instructor,
asking him why he recommended FLIRT rather than bbregister, he clarified that
4-5 years ago when he was using TRACULA for his project,
registration using bbregister either worked well for the hemispheres or for the
brainstem, but not both. He provided the slides that can be found at
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://www.dropbox.com/s/ffkz8kqqdyxojno/diff_to_anat_reg.pdf?dl=0<https://secure-web.cisco.com/1uCi2IyvVBHy3tX6oJBB9QNrkGz4S4DgkdtGlSxcNZe-0xF5zGiBkx0cNxUT6AkRgXWY1k8ZPeTsa54H_4GgkkMyhq8jHZAqOEQGQ_A0KHzqyK0RKHa_D16ybsNfPcamBZxAQGykqpzeOObVaUmSzkekbuRPcyD3n1gGz51MZFKTgdb1YSBmC4RKtSr6YKrxIewlX1p8H_ow_AWTj9cKOOIaWKCLyvc8daBWQ3xSHNChBtOVA7RtiHMJSu3kKJvPwmRiTkQ-WNRStTc0nizdwBwWJYkNt4x10wZeFzJiAQ33-FF-6bCBY6x16bB2nQ6_a8VM8XkEwW6gaiWmnbuItkw/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fffkz8kqqdyxojno%2Fdiff_to_anat_reg.pdf%3Fdl%3D0>
to share with you. He also mentioned that there is a possibility that you have
fixed this issue in the newer version of FreeSurfer. Is that true? Has this
problem been fixed in the most recent version?
Thanks again for the help.
Kindly,
Ela
____________________________________________________________________________________________________________________________________________________________________________________________________
From: Yendiki,
Anastasia<https://secure-web.cisco.com/1knn_2pxPUKVzJMh8_dhNql71BhVr-w9uwEiMOa5zQ0QQEz_OCLzXiP1vJU76vn0CD0TnILCseJTwgNUnbvBJx5M2WK8faHML9otyZK0rq_CN86mxx5jy-yCHMFGQ-WRiJX5UXcWDYTArEGX3_BE54h-UiOX0mrjwp2cEb2TaUMIydn0RHb9_Bmrxn-FUyJVc_BuCchoY88gjYZyofPtAe1gjgJZMbGzclo_kfJ2FrD1OwFpj6jh5ysfieFTcRC4Vz91J8Z3EM4j2e07RmJ9mnKSq4zHxbOvPmrwSu7Ahb6hj7_qIgKdAJCR1LHxq20rY8p89xERpx9rOp0BZFe7RMQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Yendiki%252C%2BAnastasia%2522>
Sent: Tue, 04 Jan 2022 14:21:48
-0800<https://secure-web.cisco.com/1HpQmsx8iBvKlBMBdjcVoq26jflrHCwQ1uOhmgkNfHX4mFV3cXBIkp1ARpHLIwPKnkA-Q0PUugvqFM7EyyXB7_HCatYvkOhfcYyf_PJ_Gb2dL94zhyiEI-XOXb-SGyUbuYjn_sLT0pvQuAiSMbaXVgvlTNad7cJGdeThVLpw7KAr2Xr35sMem_HrDD9oP6jTu9GMmtmPB0IXdoeDM7P7jcUL0cYwgf12qt90Qd2DJO51IWGqpjr07ULQg77LYIoQIvtqX2TtPnaB1t8W1I5XDS_4cliWEyLD7Ti-di7mPdHgluLM3ugDFWubnVszFQ2SNrrtgAt6dQ5geNiOH3vmzgA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220104>
To: elaheh.salard...@yale.edu
Subject: Re: Trac-all -prep -c error
Hi Ela - It ran fast because it's a relatively small data set (2mm resolution
and 25 directions based on the log file). So that's not a problem. No errors in
the log file as far as I can see.
I'd recommend using the default settings for both the intra- and inter-subject
registration. The new version of TRACULA is using a whole new (and improved)
atlas, so even if you use the same registration settings as someone did many
versions ago, you're not really replicating what they did (nor would it be
desirable to).
Anastasia.
________________________________
From: Salar Dini, Elaheh <elaheh.salard...@yale.edu>
Sent: Tuesday, January 4, 2022 3:40 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: Trac-all -prep -c error
Dear Anastasia,
Honestly, this was just based on our instructor's suggestion, who used to work
with you a few years back, so I just trusted his hunch. I will ask him to
clarify why he prefers this method of registration over bbregisteration.
Considering the hint you gave me in previous message, I changed the
configuration file. I am attaching it here. With this configuration file, the
trac-all -prep -c ran without any errors. However, it was all done in 40
minutes which keep me thinking if there is something wrong with it. (I set
usethalnuc = 0 for now, but I plan to change it to 1 after I have done the
thalamic sub segmentation step).
Can I ask you to check if my configuration file is correct? And if the attached
trac-all.log file looks good (not alarming)?
Thank you for your time and constant help,
Ela
____________________________________________________________________________________________________________________________________________
From: Yendiki, Anastasia
Sent: Monday, January 3, 2022
To: elaheh.salard...@yale.edu
Subject: Trac-all -prep -c error
Hi Ela - Is there a specific reason why you are not using the default method
for dMRI-to-T1 registration (bbregister, a.k.a. boundary-based registration in
the config file)?
Anastasia.
________________________________
From: Salar Dini, Elaheh
Sent: Monday, January 3, 2022 9:09 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Trac-all -prep -c error
Dear Freesurfer developers and Anastasia,
Happy new year. I am trying to run trac-all -pep -c dmriEla. dmriEla is my
config file which is also attached to this message. I am also attaching the
trac-all.log file to this email. I am getting the following error:
Segmentation fault (core dumped)
When I check the /home1/es2263/freesurfer_7.2.0/trctrain/hcp/mgh_1024/mni
folder, there is a file named acomm.bbr.prep.trk, but no file with the name
acomm.flt.prep.trk. I uninstall and reinstalled freesurfer 7.2.0, considering
there might be a problem in installation and some files might be missed, but I
still face the same error.
I'm running freesurfer on Linux Centos7, the version of freesurfer is 7.2.0 and
the installed package is freesurfer-linux-centos7_x86_64-7.2.0.tar.gz. The
installed fsl version is 6.0.5.1 .
Thank you for your help and best wishes in 2022,
Ela
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