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Hello,
I am trying to to run trac-all and I am getting the following error when using the FSL Flirt registration in the prior fitting step, due to the flt files not being available for the tract training subjects: WARN: Could not open /path/trctrain/hcp/mgh_1001/syn/acomm.flt.prep.trk for reading WARN: Error was: Can not open file WARN: Skipping to next subject
Note: The reason I am using Flirt is because BBRegister requires the lh.white and rh.white files which I don't have available as I have used third party software for the brain parcellation.
I have also had an issue with the fs_temp_file function which gives an error in cases where the subject is given as a nested folder, e.g. subject_1/subject_1_visit_1, subject_1/subject_1_visit_2 instead of subject_1_visit_1, subject_1_visit_2. This error was only noticed in the prior fitting step where the ntest was appended before subjid thus creating a file /tmp/1.subject_1/subject_1_visit_1.txt for instance causing an error.