Can you try specifying "-run 15" instead of "-run 015"? Not sure that
will make a diff, but it might.
doug
[EMAIL PROTECTED] wrote:
Hi,
Running the following command line :
unpacksdcmdir -src /media/AJB_CERV1A/07311357 -targ
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015
dti NII ajb_cerv_1a_dti.nii -unpackerr
I encountered an error of the wrong run being unpacked. Instead of 15 as
designated, 13 appears to have unpacked. This is data from our CD backup.
This does not seems to be related to environment, because I originally
tried to unpack in STD environment with same results, though all the
original analysis was done in stable3 in 2004 when the scans were
collected. The logfile is following after bugr.
Thanks in advance!
Jake
BUGR:
FREESURFER_HOME: /usr/local/freesurfer/stable3
Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717
RedHat release: CentOS release 5 (Final)
Kernel info: Linux 2.6.18-8.1.15.el5 i686
NMR Center info (/space/freesurfer exists):
machine: striatum
SUBJECTS_DIR: /space/sake/3/users/inverse/subjects
PWD: /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti
------------------------------------------------
Log file created by unpacksdcmdir
$Id: unpacksdcmdir,v 1.12 2006/01/24 18:04:33 greve Exp $
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/unpack.log
/autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti
Mon Nov 3 14:19:09 EST 2008
-src /media/AJB_CERV1A/07311357 -targ
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015
dti NII ajb_cerv_1a_dti.nii -unpackerr
dicomdir /media/AJB_CERV1A/07311357
Scanning source directory ...
INFO: summary file is
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile
INFO: status file is
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status
INFO: scanning path to Siemens DICOM DIR:
/media/AJB_CERV1A/07311357
INFO: Found 1758 files in /media/AJB_CERV1A/07311357
INFO: counting Siemens Files
$Id: mri_parse_sdcmdir.c,v 1.13.2.1 2006/05/15 21:42:35 greve Exp $
cwd /autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti
cmdline --sortbyrun --d /media/AJB_CERV1A/07311357 --o
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile
--status
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status
sysname Linux
hostname striatum
machine i686
user jake
INFO: found 1756 Siemens Files
INFO: scanning info from Siemens Files
INFO: status file is
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_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
INFO: found 1756 Siemens files
syngo MR 2004A 4VA25A
Sorting
Assigning Run Numbers
RunNo = 0
RunNo = 1
RunNo = 2
RunNo = 3
RunNo = 4
RunNo = 5
RunNo = 6
RunNo = 7
RunNo = 8
RunNo = 9
RunNo = 10
RunNo = 11
RunNo = 12
RunNo = 13
RunNo = 14
WARNING: Run 11 appears to be truncated
Files Found: 78, Files Expected (lRep+1): 126
FileName /media/AJB_CERV1A/07311357/58851927
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Allegra
PatientName ajb_cerv_1a
Date and time
StudyDate 20040731
StudyTime 121222.984000
SeriesTime 130908.562000
AcqTime 130848.812487
Acquisition parameters
PulseSeq epfid2d1_64
Protocol ge_functionals
PhEncDir COL
EchoNo 0
FlipAngle 90
EchoTime 30
InversionTime 30
RepetitionTime 2500
PhEncFOV 200
ReadoutFOV 200
Image information
RunNo 10
SeriesNo 11
ImageNo 1
NImageRows 384
NImageCols 384
NFrames 78
SliceArraylSize 30
IsMosaic 1
ImgPos 581.7606 607.9159 80.1682
VolRes 3.1250 3.1250 5.0000
VolDim 64 64 30
Vc -0.9896 -0.0181 -0.1426
Vr 0.0368 -0.9909 -0.1294
Vs -0.1389 -0.1333 0.9813
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
WARNING: Run 15 appears to be truncated
Files Found: 70, Files Expected (lRep+1): 1
FileName /media/AJB_CERV1A/07311357/58844259
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Allegra
PatientName ajb_cerv_1a
Date and time
StudyDate 20040731
StudyTime 121222.984000
SeriesTime 134037.953000
AcqTime 134005.220012
Acquisition parameters
PulseSeq ep_b0#0
Protocol DIFFUSION_HighRes
PhEncDir COL
EchoNo 0
FlipAngle 90
EchoTime 83
InversionTime 83
RepetitionTime 7900
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 14
SeriesNo 15
ImageNo 1
NImageRows 1024
NImageCols 1024
NFrames 70
SliceArraylSize 64
IsMosaic 1
ImgPos 993.7068 1043.8300 171.7054
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 64
Vc -0.9896 -0.0181 -0.1426
Vr 0.0300 -0.9962 -0.0813
Vs -0.1405 -0.0848 0.9864
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
Done scanning Mon Nov 3 14:24:42 EST 2008
------------------------------------------
1 circle_localizer ok 256 256 3 1 58867961
2 AAScout ok 128 128 128 2 58867988
3 t1_mprage_sag ok 256 256 128 1 58865756
4 t1_mprage_sag ok 256 256 128 1 58863603
5 ep2d_t1w ok 64 64 30 1 58859483
6 t2_HI_RES ok 448 444 30 1 58859933
7 AAScout ok 128 128 128 2 58860380
8 circle_localizer ok 256 256 3 1 58855710
9 ge_functionals ok 64 64 30 174 58855738
10 ge_functionals ok 64 64 30 174 58852366
11 ge_functionals err 64 64 30 78 58851927
12 ge_functionals ok 64 64 30 126 58850048
13 ge_functionals ok 64 64 30 126 58848889
14 ge_functionals ok 64 64 30 174 58844698
15 DIFFUSION_HighRes err 128 128 64 70 58844259
sortmethod fsfast
unpacking config ------------------
{015 dti NII ajb_cerv_1a_dti.nii}
-----------------------------------
---------------------------------------------------------
Run 015 -----------------------------------------
Mon Nov 3 14:24:43 EST 2008
015 dti NII ajb_cerv_1a_dti.nii
Files In Run: ---------------
58848889 58848904 58848919 58848934 58848949 58848964 58848979 58848994
58849009 58849024 58849039 58849054 58849069 58849084 58846067 58846082
58846097 58846112 58846127 58846142 58846157 58846172 58846187 58846202
58846217 58846232 58846247 58846262 58846277 58846292 58846307 58846322
58846337 58846352 58846367 58846382 58846397 58846412 58846427 58846442
58846457 58846472 58846487 58846502 58846517 58846532 58846547 58846562
58846577 58846592 58846607 58846622 58846637 58846652 58846667 58846682
58846697 58846712 58846727 58846742 58846757 58846772 58846787 58846802
58846817 58846832 58846847 58846862 58846877 58846892 58846907 58846922
58846937 58846952 58846967 58846982 58846997 58847012 58847027 58847042
58847057 58847072 58847087 58847102 58847117 58847132 58847147 58847162
58847177 58847192 58847207 58847222 58847237 58847252 58847267 58847282
58847297 58847312 58847327 58847342 58847357 58847372 58847387 58847402
58847417 58847432 58847447 58847462 58847477 58847492 58847507 58847522
58847537 58847552 58844518 58844533 58844548 58844563 58844578 58844593
58844608 58844623 58844638 58844653 58844668 58844683
-----------------------------
VolRes: 3.125 3.125 4.9999980646632
------- mri_convert -------------
mri_convert /media/AJB_CERV1A/07311357/58848889
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/ajb_cerv_1a_dti.nii
--sdcmlist
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
-----------------------
mri_convert /media/AJB_CERV1A/07311357/58848889
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/ajb_cerv_1a_dti.nii
--sdcmlist
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
reading from /media/AJB_CERV1A/07311357/58848889...
INFO: found 126 files in list file
INFO: loading series header info.
RunNo = 12
INFO: sorting.
INFO: ( 64 64 30), nframes = 126, ismosaic=1
Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5
Repetition Time = 2500, TR = 2500 ms
FileName /media/AJB_CERV1A/07311357/58848889
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Allegra
PatientName ajb_cerv_1a
Date and time
StudyDate 20040731
StudyTime 121222.984000
SeriesTime 132256.718000
AcqTime 132234.949990
Acquisition parameters
PulseSeq epfid2d1_64
Protocol ge_functionals
PhEncDir COL
EchoNo 0
FlipAngle 90
EchoTime 30
InversionTime 30
RepetitionTime 2500
PhEncFOV 200
ReadoutFOV 200
Image information
RunNo 12
SeriesNo 13
ImageNo 1
NImageRows 384
NImageCols 384
NFrames 126
SliceArraylSize 30
IsMosaic 1
ImgPos 105.3537 103.3935 -55.8230
VolRes 3.1250 3.1250 5.0000
VolDim 64 64 30
Vc -0.9896 -0.0181 -0.1426
Vr 0.0368 -0.9909 -0.1294
Vs -0.1389 -0.1333 0.9813
VolCenter -0.3464 -7.5104 -9.4246
TransferSyntaxUID 1.2.840.10008.1.2.1
sagrev = 0, correv =0, trarev = 0
Vs = -0.138915 -0.133327 0.981288
INFO: no Siemens slice order reversal detected (good!).
TR=2500.00, TE=30.00, TI=30.00, flip angle=90.00
i_ras = (-0.98962, -0.0181386, -0.142559)
j_ras = (0.0368061, -0.990906, -0.129423)
k_ras = (-0.138915, -0.133327, 0.981288)
writing to
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/ajb_cerv_1a_dti.nii...
StartTime: Mon Nov 3 14:19:09 EST 2008
EndTime: Mon Nov 3 14:24:54 EST 2008
unpacksdcmdir Done
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Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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