External Email - Use Caution Hello freesurfer devs,
Thank you so much for all of your work on Tracula! I have been following this conversation (https://secure-web.cisco.com/1Ykw2-j5trx6ExR25illKidIACAuQbQ8aKBMO_GQNJvBetczSCKd1Qag-D73npLMv-T9LQAxWCim4zQwoc6bHCXKZVS5Jd0fTRVxpO4UVp_mlCXICmfC-2-_kpT9yVmCqLjkt6VEG7NQDPdD3hv6q_TY60SnhgvkRnsZnLLnLvWOmJUyFusBRgEmubU-MtEhBCIQyBsuWL0_szL_q_4DOxLyHOJkk0WLPlF2myM129BdFjJed5pB8XXflCyBcAFGpvDMmq6YjpY9cANE3dJw4ppYsj0HZW33bZNcdvB6dnJX3N0Sjg0foYmtOTBdTJE3DI8eip4eiE5jkZKmD8M3k0g/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71749.html) about an issue using flirt, and I am having a similar issue. It sounds like this user switched to bbregister, and that resolved the problem, but I was hoping to do a quick comparison between flirt and bbregister. I am running on Linux centos7 and my freesurfer build-stamp.txt is: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b. When I run trac-all -prep with flirt (setting intrareg = 2) , I get a set of errors of the following format: WARN: Could not open /export/freesurfer/freesurfer-7.2.0/trctrain/hcp/mgh_1010/syn/acomm.flt.prep.trk for reading WARN: Error was: Can not open file I think this is a result of the call the dmri_train (around line 2167 in trac-preproc on the 7.2 branch of your github). This call uses a trklist variable, which is set as follows: (around line 2109) set trklist = `printf $xspace/%s.$reg.prep.trk " $pathlist` Since I am running with flirt, the $reg here gets replaced with flt, so the code starts looking for .flt files inside the trctrain folder. As far as I can tell the trctrain directory only contains .bbr files. Should there be .flt files within this directory? Would it make sense to replace the $reg variable with a hard-coded '.bbr'? Or are the tracks that I should be using with flirt different from those that I should use with bbr? Thanks, Amy <https://secure-web.cisco.com/1Ykw2-j5trx6ExR25illKidIACAuQbQ8aKBMO_GQNJvBetczSCKd1Qag-D73npLMv-T9LQAxWCim4zQwoc6bHCXKZVS5Jd0fTRVxpO4UVp_mlCXICmfC-2-_kpT9yVmCqLjkt6VEG7NQDPdD3hv6q_TY60SnhgvkRnsZnLLnLvWOmJUyFusBRgEmubU-MtEhBCIQyBsuWL0_szL_q_4DOxLyHOJkk0WLPlF2myM129BdFjJed5pB8XXflCyBcAFGpvDMmq6YjpY9cANE3dJw4ppYsj0HZW33bZNcdvB6dnJX3N0Sjg0foYmtOTBdTJE3DI8eip4eiE5jkZKmD8M3k0g/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71749.html> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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