External Email - Use Caution Hello Freesurfer Developers, I was going to reconstruct MPRAGE images from GE 3T machine. First I used this command: *dcmunpack -src . -scanonly scan.log*
It made just *scan.log* file for me. Then I used this command: *unpacksdcmdir -src /<my dicoms pathways> -targ <my output directory> -scanonly scan.log* However, it made 3 files for me; dicomdir.sumfile, parse.status and unpack.log, but they were 0 bites. Furthermore, the following message also appeared on the terminal: *ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/ See logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for more details* I used this command for SIEMENS data and it worked. Apparently this code just works on SIEMENS data not GE. So now what is the code that I can use for GE dcm images? 1) FREESURFER Version: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 2) Platform: Ubuntu 16.04 LTS 3) unpack.log : see attached Regards -- *Maryam Tayebi* PhD Candidate of Bioengineering Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand MSc of Medical Imaging University of Manchester, Manchester, UK
Log file created by unpacksdcmdir $Id: unpacksdcmdir,v 1.25 2015/02/06 19:19:50 greve Exp $ /hpc/mtay316/tutorial4/practice_with_data//unpack.log /hpc_htom/mtay316/tutorial4/practice_with_data/dicoms Thu Nov 8 10:59:10 NZDT 2018 -src /hpc/mtay316/tutorial4/practice_with_data/dicoms/ -targ /hpc/mtay316/tutorial4/practice_with_data/ -scanonly scan.log mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/11/07-21:59:10-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: mtay316 Machine: bn390370 Platform: Linux PlatformVersion: 4.15.0-36-generic CompilerName: GCC CompilerVersion: 40400 bn390370 Linux bn390370 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux SkipMoCo 0 dicomdir /hpc/mtay316/tutorial4/practice_with_data/dicoms/ Scanning source directory ... INFO: summary file is /hpc/mtay316/tutorial4/practice_with_data//dicomdir.sumfile INFO: status file is /hpc/mtay316/tutorial4/practice_with_data//parse.status mri_parse_sdcmdir --sortbyrun --d /hpc/mtay316/tutorial4/practice_with_data/dicoms/ --o /hpc/mtay316/tutorial4/practice_with_data//dicomdir.sumfile --status /hpc/mtay316/tutorial4/practice_with_data//parse.status INFO: scanning path to Siemens DICOM DIR: /hpc/mtay316/tutorial4/practice_with_data/dicoms INFO: Found 175 files in /hpc/mtay316/tutorial4/practice_with_data/dicoms INFO: counting Siemens Files $Id: mri_parse_sdcmdir.c,v 1.22 2015/05/21 16:37:12 greve Exp $ cwd /hpc_htom/mtay316/tutorial4/practice_with_data/dicoms cmdline --sortbyrun --d /hpc/mtay316/tutorial4/practice_with_data/dicoms/ --o /hpc/mtay316/tutorial4/practice_with_data//dicomdir.sumfile --status /hpc/mtay316/tutorial4/practice_with_data//parse.status sysname Linux hostname bn390370 machine x86_64 user mtay316 INFO: found 0 Siemens Files ERROR: scanning directory /hpc/mtay316/tutorial4/practice_with_data/dicoms ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/
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