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 warning: numerical links are often malicious: 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 warning: numerical links are often malicious: 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
------------------------------------------
  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}
-----------------------------------
---------------------------------------------------------
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
-----------------------------
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 warning: numerical links are often malicious: 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
--------------------
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> 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