Hello all,
I'm trying to unpack some old data and for a couple of sessions it is unpacking the wrong run. I just want to unpack the diffusion run. I give it the correct run number, it see's that number is the diffusion run, but unpacks another run instead. Here is the command I used:
[purkinje:pat09_sess1_dti] (nmr-stable5.1-env) unpacksdcmdir -src /space/archive/25/siemens/Allegra-20401-20040831-134936-640000 -targ /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti -run 021 dti NII pat09_sess1_dti.nii -unpackerr
Here is what is spits out:
$Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $
/autofs/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti -src /space/archive/25/siemens/Allegra-20401-20040831-134936-640000 -targ /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti -run 021 dti NII pat09_sess1_dti.nii -unpackerr
Thu Sep 29 10:12:31 EDT 2011
mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/09/29-14:12:31-GMT BuildTimeStamp: Sep 27 2011 05:57:44 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: swoodman Machine: purkinje Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400
purkinje Linux purkinje 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
Thu Sep 29 10:12:31 EDT 2011 Log File is /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/unpack.log INFO: Logfile is /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dicomdir.sumfile INFO: status file is /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/parse.status Scanning directory Thu Sep 29 10:12:31 EDT 2011 mri_parse_sdcmdir --sortbyrun --d /space/archive/25/siemens/Allegra-20401-20040831-134936-640000 --o /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dicomdir.sumfile --status /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/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 Thu Sep 29 10:20:13 EDT 2011 ------------------------------------------ 1 circle_localizer ok 256 256 3 1 640000-1-2.dcm 2 AAScout ok 128 128 128 2 640000-2-1.dcm 3 t1_mprage_sag ok 256 256 128 1 640000-3-1.dcm 4 t1_mprage_sag ok 256 256 128 1 640000-4-1.dcm 5 ep2d_t1w ok 64 64 30 1 640000-5-1.dcm 6 t2_HI_RES ok 448 444 30 1 640000-6-1.dcm 7 ge_functionals_PACE ok 64 64 30 174 640000-7-1.dcm 8 ge_functionals_PACE ok 64 64 30 174 640000-8-1.dcm 9 ge_functionals_PACE err 64 64 30 10 640000-9-1.dcm 10 ge_functionals_PACE err 64 64 30 10 640000-10-1.dcm 11 ge_functionals_PACE ok 64 64 30 174 640000-11-1.dcm 12 ge_functionals_PACE ok 64 64 30 174 640000-12-1.dcm 13 ge_functionals_PACE ok 64 64 30 174 640000-13-1.dcm 14 ge_functionals_PACE ok 64 64 30 174 640000-14-1.dcm 15 ge_functionals_PACE ok 64 64 30 174 640000-15-1.dcm 16 ge_functionals_PACE ok 64 64 30 174 640000-16-1.dcm 17 ge_functionals_PACE ok 64 64 30 174 640000-17-1.dcm 18 ge_functionals_PACE ok 64 64 30 174 640000-18-1.dcm 19 ge_functionals_PACE ok 64 64 30 174 640000-19-1.dcm 20 ge_functionals_PACE ok 64 64 30 174 640000-20-1.dcm 21 DIFFUSION_HighRes err 128 128 64 70 640000-21-1.dcm 22 DIFFUSION_VeryHighRes err 128 128 30 84 640000-22-1.dcm unpacking config ------------------ {021 dti NII pat09_sess1_dti.nii} ----------------------------------- --------------------------------------------------------- Run 021 ----------------------------------------- Thu Sep 29 10:20:13 EDT 2011 021 dti NII pat09_sess1_dti.nii mri_convert /space/archive/25/siemens/Allegra-20401-20040831-134936-640000/640000-17-1.dcm /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017/pat09_sess1_dti.nii --sdcmlist /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom
StartTime: Thu Sep 29 10:12:31 EDT 2011 EndTime: Thu Sep 29 10:20:32 EDT 2011 unpacksdcmdir Done
**and as you see if has decided to copy to run 017 and in that directory the output files are not correct.
[purkinje:pat09_sess1_dti] (nmr-stable5.1-env) ls dicomdir.sumfile dti unpack.log [purkinje:pat09_sess1_dti] (nmr-stable5.1-env) cd dti [purkinje:dti] (nmr-stable5.1-env) ls 017 seq.info [purkinje:dti] (nmr-stable5.1-env) cd 017/ [purkinje:017] (nmr-stable5.1-env) ls flf pat09_sess1_dti.nii pat09_sess1_dti.nii-infodump.dat
The bugreport:
FREESURFER_HOME: /usr/local/freesurfer/stable5_1_0
Build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514
RedHat release: CentOS release 5.5 (Final)
Kernel info: Linux 2.6.18-194.32.1.el5 x86_64
NMR Center info (/space/freesurfer exists):
machine: purkinje
SUBJECTS_DIR: /space/sake/3/users/inverse/subjects
PWD: /autofs/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017
ssh purkinje setenv SUBJECTS_DIR /space/sake/3/users/inverse/subjects cd /autofs/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017
Any advice/help is much appreciated.
Thank you!!
Sandra