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 _________________ [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.edu<http://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.
dmrirc.local
Description: dmrirc.local
dmrirc.long.subj1
Description: dmrirc.long.subj1
Fri May 30 13:22:03 EDT 2014
/data/napls_DTI/TSS/fs_tracula/scripts
/usr/local/packages/freesurfer/bin/trac-all
-prep -c dmrirc.long.subj1
Subject 01_V1000_2_01
SUBJECTS_DIR /data/napls_DTI/TSS/fs_tracula/fsrecon
FREESURFER_HOME /usr/local/packages/freesurfer-v5.3.0
Actual FREESURFER_HOME /usr/local/packages/freesurfer-v5.3.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
ychung
cns1.psych.yale.edu
Linux 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
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 1024
total used free shared buffers cached
Mem: 198019400 184183516 13835884 0 52749684 13260432
-/+ buffers/cache: 118173400 79846000
Swap: 405503996 866988 404637008
########################################
Program versions:
$Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/30-17:22:03-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: ychung Machine: cns1.psych.yale.edu Platform: Linux PlatformVersion: 3.9.10-100.fc17.x86_64 CompilerName: GCC CompilerVersion: 40400
FLIRT version 6.0
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/30-17:22:03-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: ychung Machine: cns1.psych.yale.edu Platform: Linux PlatformVersion: 3.9.10-100.fc17.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/30-17:22:03-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: ychung Machine: cns1.psych.yale.edu Platform: Linux PlatformVersion: 3.9.10-100.fc17.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/30-17:22:03-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: ychung Machine: cns1.psych.yale.edu Platform: Linux PlatformVersion: 3.9.10-100.fc17.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/30-17:22:03-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: ychung Machine: cns1.psych.yale.edu Platform: Linux PlatformVersion: 3.9.10-100.fc17.x86_64 CompilerName: GCC CompilerVersion: 40400
Linux 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
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