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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_GQNJvBetc...) 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
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