External Email - Use Caution
Hi Anastasia
Thanks so much for your reply. I have attached herewith the scripts/log file
-please let me know if you need anything else.
Regards,
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia
<ayend...@mgh.harvard.edu>
Sent: Wednesday, March 17, 2021 5:40 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA error: missing output volume name
Hi Shanika - Can you please send the full log file from scripts/trac-all.log?
It's hard to figure out what causes the error without seeing the full output.
Nothing looks unusual in the config file.
Thanks,
Anastasia.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody
<shanika.jayak...@einsteinmed.org>
Sent: Wednesday, March 17, 2021 4:04 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA error: missing output volume name
External Email - Use Caution
External Email - Use Caution
Dear FreeSurfer team
I have been running TRACULA for some time now but recently, I come across a
message "missing output volume name" and I cannot do preprocessing in new or
old subjects (even subjects who completed preprocessing without error)
I have not made any change to the configuration files. It is the same format
that I have been using.
Any advice on this is appreciated. I have attached one of the configuration
files.
Thanks,
Shanika
Wed Mar 17 15:41:52 EDT 2021
/home/helena/Documents/freesurfer/subjects
/home/helena/Documents/freesurfer/bin/trac-all
-prep -c Configurationfile_Osh.txt
Subject 30024
SUBJECTS_DIR /home/helena/Documents/freesurfer/subjects
FREESURFER_HOME /home/helena/Documents/freesurfer
Actual FREESURFER_HOME /home/helena/Documents/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
helena
peter-ThinkStation-P520
Linux peter-ThinkStation-P520 4.15.0-137-generic #141~16.04.1-Ubuntu SMP Wed Feb 24 10:47:15 UTC 2021 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 642289
maxlocks unlimited
maxsignal 642289
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 164636836 4208204 156505448 104888 3923184 158875624
Swap: 1000444 0 1000444
########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info
ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/17-19:41:52-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: helena Machine: peter-ThinkStation-P520 Platform: Linux PlatformVersion: 4.15.0-137-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/17-19:41:52-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: helena Machine: peter-ThinkStation-P520 Platform: Linux PlatformVersion: 4.15.0-137-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/17-19:41:52-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: helena Machine: peter-ThinkStation-P520 Platform: Linux PlatformVersion: 4.15.0-137-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/17-19:41:52-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: helena Machine: peter-ThinkStation-P520 Platform: Linux PlatformVersion: 4.15.0-137-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/17-19:41:52-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: helena Machine: peter-ThinkStation-P520 Platform: Linux PlatformVersion: 4.15.0-137-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/17-19:41:52-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: helena Machine: peter-ThinkStation-P520 Platform: Linux PlatformVersion: 4.15.0-137-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/17-19:41:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: helena Machine: peter-ThinkStation-P520 Platform: Linux PlatformVersion: 4.15.0-137-generic CompilerName: GCC CompilerVersion: 40400
New invocation of trac-preproc
helena
peter-ThinkStation-P520
Linux peter-ThinkStation-P520 4.15.0-137-generic #141~16.04.1-Ubuntu SMP Wed Feb 24 10:47:15 UTC 2021 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 642289
maxlocks unlimited
maxsignal 642289
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 164636836 4209220 156476084 104888 3951532 158874312
Swap: 1000444 0 1000444
#-------------------------------------
/home/helena/Documents/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Wed Mar 17 15:41:53 EDT 2021
mri_convert --bvec-voxel /home/helena/Documents/freesurfer/subjects/30024/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /home/helena/Documents/freesurfer/subjects/30024/dmri/dwi_orig.nii.gz
mri_convert.bin: missing output volume name
type mri_convert.bin -u for usage
Linux peter-ThinkStation-P520 4.15.0-137-generic #141~16.04.1-Ubuntu SMP Wed Feb 24 10:47:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Mar 17 15:41:53 EDT 2021
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