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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