External Email - Use Caution 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 https://secure-web.cisco.com/1oQ069dBAr-aqyrA-2ybD146HtFLwzskO-LkSCf4geRQW6-jjJsW3q3TJ5J_cwyWBUFHaHgRvxJ8mD-ihQW76B1_yzpRAqVVBzLk58Uf5riUSSfNJuP6mnd_a5oSnU_HOF3gBAKoqEI0tLHPsGN7mtrJg4nhNxsKW7QO619cGgHfw7vvTPDlfZldBYbfOfBTOaxJB3nuMoC5PvwKVJI7xMlLVRzgR9zYcSBre3bvUJd4pUGSf6grxttnMYW9P2zXNNy88Os-WtSUa7y-DxGQkRpPiRTzMju5vrQujQSHfPfmHLULx4ACbI7-VCFTnYDb9FumypRwkRdrsMBNL19pDhw/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/18p--HnLUoyD5WB8i6NS-wIUD7ruIZkXvVCuRPYdPT4cLvnxypVuKIVRpfa2JmFWe-0HQO9jlRvjyaof9yQYk7INBdwjxKQVpImeQ-uUeM7aAF2KyJn4PkD_K2LRXCc0g7jlMj5sHh_YSYpULOX7lBLB8oxO7drNN7BherQoIxOCGEgh9NqUxSfEI71b7qnrpIh5Yi-kDHh3hmUOCQBuUIGI_MLmh2Iv4SaAFHdBTLrwr-rIqXu5mQ45LvDpcNTt2S_VzvaP9eoc693r4sX7Yd5Atd-c9g5jSRaVV3ZbQ8s8SfH-9jZ3r3esbVZyZr-_2uZChsGSkfPtzKGLQIxhL8A/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/1J1nc2rG5pbvDDNxOyMPhWcxyPoihvCSxGUSPWNZUNEZ08O2HwoZ2uORo6JonotiIjbWt46BP22Qw8EjUjgbAom64A1qwvFaUXSvMEmmFRhRXY94mDenmWug2jSAW9p62NPw9_SsWfOsBFKpofgd0tA6cyUH9rhguZ6r3a7xz89cpsKS3K3CSnwcRE9Chdk0tjIbQ7L8gmeJRbhUbZLfTOpDZ-Ro7iOwV1yCn2z2vxEZ-_OyIsQwxtMKD7XiF8J1lDheSF2-qsCvN8nhsSUVzH4ZvsySAw73Rs0zPVJTtIPf8tSmG6L1qT8Zw6f3Brihs5lyRSN3GSEINXmH9yB2fJQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220104> To: [email protected] 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 <[email protected]> Sent: Tuesday, January 4, 2022 3:40 PM To: Freesurfer support list <[email protected]> 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: [email protected] 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 <[email protected]> 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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