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

Sent: Sun, 09 Jan 2022 19:06:53 -0800

To: elaheh.salardini@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.salardini@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

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
Sent: Tue, 04 Jan 2022 14:21:48 -0800
To: elaheh.salardini@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.salardini@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.salardini@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