Hi Anastasia

I switched from FS v.5.2 to v.5.3 and I am still having this error when running TRACULA longitudinal freesurfer stream despite running with freesurfer v5.3 (both recon-all and trac-all). I am sending along the dmrirc file and the log file. Could you check what may be causing this problem?

for testing subjects I am only running one subject with two timepoints.

01_V1000_2_01 # timepoint 1 01_V1000_2_02 # timepoint 2

another question I have is that in the dmrirc file, can we also define multiple bval files? (like how in the example-dmrirc long- you can set multiple bvecs.txt using 'set bveclist'? In the example, option for specifying multiple bval files is not shown. Thank you so much for your time.

Best, Yoon

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[ychung@cns1 scripts]$ trac-all -prep -c dmrirc.long.subj1 Too many )'s. INFO: SUBJECTS_DIR is /data/napls_DTI/TSS/fs_tracula/fsrecon INFO: Diffusion root is /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI Actual FREESURFER_HOME /usr/local/packages/freesurfer-v5.3.0 trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/trac-all.cmd ; trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/trac-all.cmd ; trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/trac-all.cmd ; ERROR: flag ; unrecognized -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/trac-all.cmd ; trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/trac-all.cmd ; trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/trac-all.cmd ; Linux cns1.psych.yale.eduhttp://cns1.psych.yale.edu/ 3.9.10-100.fc17.x86_64 #1 SMP Sun Jul 14 01:31:27 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri May 30 13:22:04 EDT 2014

IsRunningFile: Undefined variable.