Hi Adrienne, you only have run 6 listed in your cfg file, so it's only unpacking run 6.

doug

Adrienne McCallister wrote:

Hello,

Below is the unpacklog from the command:

the command used was: unpacksdcmdir -src . -targ /autofs/space/jizo_001/users/RR-MBSR/002-ND_post -cfg /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/mycfg I was sitting in the /autofs/space/archive_166/siemens/Avanto-25096-20080621-122038-263000 directory.

Thanks!!

Log file created by unpacksdcmdir $Id: unpacksdcmdir,v MailScanner has detected a possible fraud attempt from "1.19.2.2" claiming to be MailScanner warning: numerical links are often malicious: 1.19.2.2 http://1.19.2.2 2008/03/11 19:56:38 nicks Exp $ /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/unpack.log /autofs/space/archive_166/siemens/Avanto-25096-20080621-122038-263000 Tue Aug 26 16:46:39 EDT 2008 -src . -targ /autofs/space/jizo_001/users/RR-MBSR/002-ND_post -cfg /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/mycfg mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2008/08/26-20:46:39-GMT BuildTimeStamp: Aug 21 2008 19:03:45 CVS: $Id: mri_convert.c,v MailScanner has detected a possible fraud attempt from "1.146.2.3" claiming to be MailScanner warning: numerical links are often malicious: 1.146.2.3 http://1.146.2.3 2008/08/11 22:18:58 nicks Exp $ User: adrienne Machine: jizo Platform: Linux PlatformVersion: 2.6.9-67.ELsmp CompilerName: GCC CompilerVersion: 30400 jizo Linux jizo 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64 x86_64 x86_64 GNU/Linux SkipMoCo 0 dicomdir . Scanning source directory ... INFO: summary file is /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/dicomdir.sumfile INFO: status file is /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/parse.status mri_parse_sdcmdir --sortbyrun --d . --o /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/dicomdir.sumfile --status /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/parse.status INFO: scanning path to Siemens DICOM DIR: . INFO: Found 1653 files in . INFO: counting Siemens Files $Id: mri_parse_sdcmdir.c,v 1.18 2007/04/27 02:23:42 nicks Exp $ cwd /autofs/space/archive_166/siemens/Avanto-25096-20080621-122038-263000 cmdline --sortbyrun --d . --o /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/dicomdir.sumfile --status /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/parse.status sysname Linux hostname jizo machine x86_64 user adrienne INFO: found 1651 Siemens Files INFO: scanning info from Siemens Files INFO: status file is /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/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 1651 Siemens files syngo MR B15 Could not parse NUMARIS version string syngo MR B15 found in dicom tag 18,1020 (len = 3 != 6) Sorting Assigning Run Numbers RunNo = 0 RunNo = 1 RunNo = 2 RunNo = 3 RunNo = 4 RunNo = 5 RunNo = 6 RunNo = 7 RunNo = 8 Done scanning Tue Aug 26 16:47:33 EDT 2008

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1 localizer ok 512 512 3 1 263000-000001-000002.dcm 2 AAScout ok 128 128 128 2 263000-000002-000001.dcm 3 T1_MPRAGE_sag ok 256 256 128 1 263000-000003-000001.dcm 4 localizer ok 512 512 3 1 263000-000004-000002.dcm 5 AAScout ok 128 128 128 2 263000-000005-000001.dcm 6 T1_MPRAGE_sag ok 256 256 128 1 263000-000006-000001.dcm 7 T1_MPRAGE_sag ok 256 256 128 1 263000-000007-000001.dcm 8 post_ep2d_t1w ok 64 64 25 1 263000-000008-000001.dcm 9 RRMBSR ok 64 64 25 724 263000-000009-000001.dcm sortmethod fsfast unpacking config ------------------ {6 bold SPM pre_ge_functionals}

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Run 6 ----------------------------------------- Tue Aug 26 16:47:33 EDT 2008 6 bold SPM pre_ge_functionals Files In Run: --------------- 263000-000006-000001.dcm 263000-000006-000002.dcm 263000-000006-000003.dcm 263000-000006-000004.dcm 263000-000006-000005.dcm 263000-000006-000006.dcm 263000-000006-000007.dcm 263000-000006-000008.dcm 263000-000006-000009.dcm 263000-000006-000010.dcm 263000-000006-000011.dcm 263000-000006-000012.dcm 263000-000006-000013.dcm 263000-000006-000014.dcm 263000-000006-000015.dcm 263000-000006-000016.dcm 263000-000006-000017.dcm 263000-000006-000018.dcm 263000-000006-000019.dcm 263000-000006-000020.dcm 263000-000006-000021.dcm 263000-000006-000022.dcm 263000-000006-000023.dcm 263000-000006-000024.dcm 263000-000006-000025.dcm 263000-000006-000026.dcm 263000-000006-000027.dcm 263000-000006-000028.dcm 263000-000006-000029.dcm 263000-000006-000030.dcm 263000-000006-000031.dcm 263000-000006-000032.dcm 263000-000006-000033.dcm 263000-000006-000034.dcm 263000-000006-000035.dcm 263000-000006-000036.dcm 263000-000006-000037.dcm 263000-000006-000038.dcm 263000-000006-000039.dcm 263000-000006-000040.dcm 263000-000006-000041.dcm 263000-000006-000042.dcm 263000-000006-000043.dcm 263000-000006-000044.dcm 263000-000006-000045.dcm 263000-000006-000046.dcm 263000-000006-000047.dcm 263000-000006-000048.dcm 263000-000006-000049.dcm 263000-000006-000050.dcm 263000-000006-000051.dcm 263000-000006-000052.dcm 263000-000006-000053.dcm 263000-000006-000054.dcm 263000-000006-000055.dcm 263000-000006-000056.dcm 263000-000006-000057.dcm 263000-000006-000058.dcm 263000-000006-000059.dcm 263000-000006-000060.dcm 263000-000006-000061.dcm 263000-000006-000062.dcm 263000-000006-000063.dcm 263000-000006-000064.dcm 263000-000006-000065.dcm 263000-000006-000066.dcm 263000-000006-000067.dcm 263000-000006-000068.dcm 263000-000006-000069.dcm 263000-000006-000070.dcm 263000-000006-000071.dcm 263000-000006-000072.dcm 263000-000006-000073.dcm 263000-000006-000074.dcm 263000-000006-000075.dcm 263000-000006-000076.dcm 263000-000006-000077.dcm 263000-000006-000078.dcm 263000-000006-000079.dcm 263000-000006-000080.dcm 263000-000006-000081.dcm 263000-000006-000082.dcm 263000-000006-000083.dcm 263000-000006-000084.dcm 263000-000006-000085.dcm 263000-000006-000086.dcm 263000-000006-000087.dcm 263000-000006-000088.dcm 263000-000006-000089.dcm 263000-000006-000090.dcm 263000-000006-000091.dcm 263000-000006-000092.dcm 263000-000006-000093.dcm 263000-000006-000094.dcm 263000-000006-000095.dcm 263000-000006-000096.dcm 263000-000006-000097.dcm 263000-000006-000098.dcm 263000-000006-000099.dcm 263000-000006-000100.dcm 263000-000006-000101.dcm 263000-000006-000102.dcm 263000-000006-000103.dcm 263000-000006-000104.dcm 263000-000006-000105.dcm 263000-000006-000106.dcm 263000-000006-000107.dcm 263000-000006-000108.dcm 263000-000006-000109.dcm 263000-000006-000110.dcm 263000-000006-000111.dcm 263000-000006-000112.dcm 263000-000006-000113.dcm 263000-000006-000114.dcm 263000-000006-000115.dcm 263000-000006-000116.dcm 263000-000006-000117.dcm 263000-000006-000118.dcm 263000-000006-000119.dcm 263000-000006-000120.dcm 263000-000006-000121.dcm 263000-000006-000122.dcm 263000-000006-000123.dcm 263000-000006-000124.dcm 263000-000006-000125.dcm 263000-000006-000126.dcm 263000-000006-000127.dcm 263000-000006-000128.dcm

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VolRes: 1 1 1.3300000429153 ------- mri_convert ------------- mri_convert ./263000-000006-000001.dcm /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/pre_ge_functionals --sdcmlist /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/flf -ot spm

--nspmzeropad 3 --in_type siemens_dicom

mri_convert ./263000-000006-000001.dcm /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/pre_ge_functionals --sdcmlist /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/flf -ot spm --nspmzeropad 3 --in_type siemens_dicom mri_convert ./263000-000006-000001.dcm /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/pre_ge_functionals --sdcmlist /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/flf -ot spm --nspmzeropad 3 --in_type siemens_dicom $Id: mri_convert.c,v MailScanner has detected a possible fraud attempt from "1.146.2.3" claiming to be MailScanner warning: numerical links are often malicious: 1.146.2.3 http://1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from ./263000-000006-000001.dcm... INFO: found 128 files in list file INFO: loading series header info.

RunNo = 5 INFO: sorting. INFO: (256 256 128), nframes = 1, ismosaic=0 AutoAlign matrix detected AutoAlign Matrix --------------------- 0.999 -0.024 0.042 -6.365; 0.029 0.991 -0.128 -13.683; -0.038 0.129 0.991 -2.572; 0.000 0.000 0.000 1.000;

FileName ./263000-000006-000001.dcm Identification NumarisVer syngo MR B15 ScannerModel Avanto PatientName 002-ND-post_lazar Date and time StudyDate 20080621 StudyTime 122038.263000 SeriesTime 125014.602000 AcqTime 124127.222500 Acquisition parameters PulseSeq *tfl3d1_ns Protocol T1_MPRAGE_sag PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 3.39 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 5 SeriesNo 6 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 85.5418 148.1949 113.2592 VolRes 1.0000 1.0000 1.3300 VolDim 256 256 128 Vc 0.0325 -0.9955 -0.0887 Vr 0.0356 0.0899 -0.9953 Vs -0.9988 -0.0292 -0.0384 VolCenter 9.2392 29.7880 -28.7659 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2730.00, TE=3.39, TI=1000.00, flip angle=7.00 i_ras = (0.0324721, -0.995527, -0.0887199) j_ras = (0.0356403, 0.0898636, -0.995316) k_ras = (-0.998837, -0.029158, -0.038399) writing to /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/pre_ge_functionals... Analyze Output Matrix 0.032 0.036 -1.328 86.802; -0.996 0.090 -0.039 149.139; -0.089 -0.995 -0.051 114.394; 0.000 0.000 0.000 1.000; No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for are: x_r = 0.0325, y_r = 0.0356, z_r = -0.9988, c_r = 9.2392 x_a = -0.9955, y_a = 0.0899, z_a = -0.0292, c_a = 29.7880 x_s = -0.0887, y_s = -0.9953, z_s = -0.0384, c_s = -28.7659

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INFO: set hdr.hist.orient to 'transverse unflipped'

StartTime: Tue Aug 26 16:46:39 EDT 2008 EndTime: Tue Aug 26 16:47:40 EDT 2008 unpacksdcmdir Done

On Wed, Aug 27, 2008 at 11:06 AM, Allison Stevens <astevens@nmr.mgh.harvard.edu mailto:astevens@nmr.mgh.harvard.edu> wrote:

Adrienne,
Please send the exact command line you used to the list.
Allison


On Wed, 27 Aug 2008, Adrienne McCallister wrote:

    Hello,

    I am trying to unpack dicom files for a specific subject.
    THese files are
    located at:

    /space/archive/166/siemens/Avanto-25096-20080621-122038-263000

    I have tried both the unpacksdcmdir command as well as a dicom
    import
    directly into SPM. The unpacksdcmdir command did appear to
    work but there
    was only 1 functional scan unpacked. When I did the SPM
     import, the
    structurals seemed to import but again the functionals looked
    really
    strange. They just look like a white diagonal line going
    through the black
    background.

    These files may just be unusable but I wanted to ask if you
    had any input
    before I give up. Thanks for your help.

    Sincerely,

    Adrienne McCallister

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