Freesurfer team,
Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and v5.3.0.
The command line is:
unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK
And I get the error message:
$Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $
/home/jbang/Projects/replay/log -src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ /home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg /home/jbang/Projects/replay/log//
Wed Feb 3 18:12:41 EST 2016
mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2016/02/03-23:12:41-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: jbang Machine: cpu166.cabiatl.com Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400
cpu166.cabiatl.com Linux cpu166.cabiatl.com 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
Wed Feb 3 18:12:41 EST 2016 Log File is /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log INFO: Logfile is /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile INFO: status file is /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status Scanning directory Wed Feb 3 18:12:41 EST 2016 mri_parse_sdcmdir --sortbyrun --d /home/jbang/Projects/replay/epi//replay01/DICOM/day1 --o /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile --status /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Wed Feb 3 18:17:33 EST 2016 ------------------------------------------ 2 localizer ok 512 512 3 1 00002_loc02.dcm 3 fMRI_physio_1_decoder ok 74 74 33 150 00001_dec01.dcm 5 fMRI_physio_2_decoder ok 74 74 33 150 00001_dec02.dcm 7 fMRI_physio_3_decoder ok 74 74 33 150 00001_dec03.dcm 9 fMRI_physio_4_decoder ok 74 74 33 150 00001_dec04.dcm 11 fMRI_physio_5_decoder ok 74 74 33 150 00001_dec05.dcm 13 fMRI_physio_6_decoder ok 74 74 33 150 00001_dec06.dcm 15 fMRI_physio_7_decoder ok 74 74 33 150 00001_dec07.dcm 17 fMRI_physio_8_decoder ok 74 74 33 150 00001_dec08.dcm 19 fMRI_physio_9_decoder ok 74 74 33 150 00001_dec09.dcm 21 fMRI_physio_10_decoder ok 74 74 33 150 00001_dec10.dcm 23 fMRI_physio_1_retinotopy ok 74 74 33 120 00001_retino01.dcm 25 fMRI_physio_2_retinotopy ok 74 74 32 120 00001_retino02.dcm 27 fMRI_physio_3_retinotopy ok 74 74 32 120 00001_retino03.dcm 29 fMRI_physio_4_retinotopy ok 74 74 32 120 00001_retino04.dcm 31 fMRI_physio_5_retinotopy ok 74 74 32 120 00001_retino05.dcm 35 T1_MEMPRAGE ok 256 256 176 4 00001_T1_MEMPRAGE_35.dcm 36 T1_MEMPRAGE ok 256 256 176 1 00001_RMS.dcm error reading "file4": illegal operation on a directory while executing "gets $FileId line" (procedure "ReadSeqCfg" line 11) invoked from within "ReadSeqCfg $seqcfgfile" invoked from within "if { [info exists seqcfgfile] } { set SeqCfgList [ReadSeqCfg $seqcfgfile]; }" (file "/home/jbang/freesurfer//bin/unpacksdcmdir.tcl" line 1048)
This same error message appeared on both v4.5.0 and v5.3.0.
Do you have any clue to fix it?
Thank you for your help.
Best, Ji Won