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
------------------------------------------
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 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
--------------------
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
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
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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MGH-NMR Center
[EMAIL PROTECTED]
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