Can you run that mri_convert command by itself and send me the terminal
output?
On 05/10/2017 02:26 PM, Dillon, Daniel G. wrote:
Hi everyone. I’m unpacking dicoms collected on a 3T Tim Trio and I’m
getting segmentation errors (see below) with two of ~80 subjects when
using either unpacksdcmdir or dcmunpack (I’ve tried both commands with
FreeSurfer 5.3.0 and 5.3.1, running on the Harvard NCF cluster). I’m
not sure what to try next, hoping to get some advice . . . I don’t
know that anything went wrong with the scans but it’s odd that only
these two subjects are failing. Any ideas for a fix?
Thanks in advance,
Dan Dillon
Here’s the command and output with unpacksdcmdir:
unpacksdcmdir -src 151027_RMD057/RAW/ -targ 151027_RMD057 -fsfast
-cfg 151027_RMD057/151027_RMD057.cfg
$Id: unpacksdcmdir,v 1.19.2.1 2007/09/19 14:34:42 greve Exp $
/net/rcss2/srv/export/ncf_anl/share_root/anl01/RMD
-src 151027_RMD057/RAW/ -targ 151027_RMD057 -fsfast -cfg
151027_RMD057/151027_RMD057.cfg
Wed May 10 12:20:08 EDT 2017
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp:
2017/05/10-16:20:08-GMT BuildTimeStamp: Dec
16 2007 07:41:05 CVS: $Id: mri_convert.c,v 1.146.2.1 2007/11/30
23:18:44 greve Exp $ User: ddillon Machine:
ncfc22.rc.fas.harvard.edu
<http://ncfc22.rc.fas.harvard.edu><http://ncfc22.rc.fas.harvard.edu/>
Platfor
m: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64
CompilerName: GCC CompilerVersion: 30400
ncfc22.rc.fas.harvard.edu
<http://ncfc22.rc.fas.harvard.edu><http://ncfc22.rc.fas.harvard.edu/>
Linux ncfc22.rc.fas.harvard.edu
<http://ncfc22.rc.fas.harvard.edu><http://ncfc22.rc.fas.harvard.edu/>
2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux
Wed May 10 12:20:08 EDT 2017
Log File is 151027_RMD057/unpack.log
INFO: Logfile is 151027_RMD057/unpack.log
SkipMoCo 0
Scanning source directory ...
INFO: summary file is 151027_RMD057/dicomdir.sumfile
INFO: status file is 151027_RMD057/parse.status
Scanning directory Wed May 10 12:20:09 EDT 2017
mri_parse_sdcmdir --sortbyrun --d 151027_RMD057/RAW/ --o
151027_RMD057/dicomdir.sumfile --status 151027_RMD057/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 Wed May 10 12:22:14 EDT 2017
------------------------------------------
5 T1_MEMPRAGE ok 192 192 144 1
151027_RMD057.MR.INVESTIGATORS_Dillon.5.1.20151027.152735.1oe820t.dcm
6 T2_SPACE ok 192 192 144 1
151027_RMD057.MR.INVESTIGATORS_Dillon.6.1.20151027.152735.4qpapf.dcm
17 REVMEM_01 ok 72 72 47 290
151027_RMD057.MR.INVESTIGATORS_Dillon.17.1.20151027.152735.7xk08n.dcm
19 REVMEM_02 ok 72 72 47 290
151027_RMD057.MR.INVESTIGATORS_Dillon.19.1.20151027.152735.xgrals.dcm
21 PST_01 ok 72 72 47 170
151027_RMD057.MR.INVESTIGATORS_Dillon.21.1.20151027.152735.1trnf8q.dcm
23 PST_02 ok 72 72 47 170
151027_RMD057.MR.INVESTIGATORS_Dillon.23.1.20151027.152735.1q4ykwt.dcm
25 PST_03 ok 72 72 47 170
151027_RMD057.MR.INVESTIGATORS_Dillon.25.1.20151027.152735.3k8rgn.dcm
27 PST_04 ok 72 72 47 170
151027_RMD057.MR.INVESTIGATORS_Dillon.27.1.20151027.152735.wkcxen.dcm
unpacking config ------------------
{5 3danat nii T1.nii} {6 3danat nii T2.nii} {17 RevMem nii f.nii}
{19 RevMem nii f.nii} {21 PST nii f.nii} {23 PST nii f.nii} {25
PST nii f.nii}
{27 PST nii f.nii}
-----------------------------------
---------------------------------------------------------
Run 5 -----------------------------------------
Wed May 10 12:22:14 EDT 2017
5 3danat nii T1.nii
mri_convert
151027_RMD057/RAW//151027_RMD057.MR.INVESTIGATORS_Dillon.5.1.20151027.152735.1oe820t.dcm
151027_RMD057/3danat/005/T1.nii --sdcmlist 1
51027_RMD057/3danat/005/flf -ot nii --nspmzeropad 3 --in_type
siemens_dicom
ERROR: mri_convert
child killed: segmentation violation
Here’s the command and output with dcmunpack:
dcmunpack -src 151027_RMD057/RAW/ -targ 151027_RMD057 -fsfast -run
5 3danat nii T1.nii
/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/5.3.1/bin/dcmunpack
-src 151027_RMD057/RAW/ -targ 151027_RMD057 -fsfast -run 5 3danat
nii T1.nii
-rwxr-xr-x 1 nrgadmin nrg 23416 Feb 19 2015
/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/5.3.1/bin/dcmunpack
---------------------------------------
1 5 3danat T1 0 0
---------------------------------------
Searching for matching files
Wed May 10 13:34:44 EDT 2017
Wed May 10 13:34:44 EDT 2017
Found 1549 total files.
Interrogating each and every one of them.
Be patient.
If you have collected the data in the Martinos center, this
will run faster if you kill this job and re-run with -martinos
Found 8 unique series: 5 6 17 19 21 23 25 27
Subject 151027_RMD057
Date 20151027
Time 152735.343000
Institution
5 T1_MEMPRAGERMS 1.54 2200 7 1.1979166269302\1.1979166269302 ROW
651
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.5.124.20151027.152735.14a3j6a.dcm
6 T2_SPACE 327 2800 120 1.1979166269302\1.1979166269302 ROW 651
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.6.109.20151027.152735.hkvqu7.dcm
17 REVMEM_01 30 3000 75 unknown COL 2240
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.17.53.20151027.152735.q6qzzg.dcm
19 REVMEM_02 30 3000 75 unknown COL 2240
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.19.118.20151027.152735.csj5a8.dcm
21 PST_01 30 3000 75 unknown COL 2240
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.21.141.20151027.152735.61ysw7.dcm
23 PST_02 30 3000 75 unknown COL 2240
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.23.108.20151027.152735.1g8omw.dcm
25 PST_03 30 3000 75 unknown COL 2240
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.25.149.20151027.152735.waf4h2.dcm
27 PST_04 30 3000 75 unknown COL 2240
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.27.167.20151027.152735.b9fgot.dcm
mri_convert
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.5.124.20151027.152735.14a3j6a.dcm
151027_RMD057/3danat/005/T1.nii --nskip 0 --ndrop 0
nskip = 0
ndrop = 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.5.124.20151027.152735.14a3j6a.dcm...
Getting Series No
INFO: Found 1550 files in 151027_RMD057/RAW
INFO: Scanning for Series Number 5
Scanning Directory
INFO: found 144 files in series
INFO: loading series header info.
RunNo = 4
INFO: sorting.
INFO: (192 192 144), nframes = 1, ismosaic=0
PE Dir ROW ROW
AutoAlign matrix detected
AutoAlign Matrix ---------------------
0.997 -0.028 -0.069 3.361;
0.019 0.992 -0.128 -12.399;
0.072 0.127 0.989 0.552;
0.000 0.000 0.000 1.000;
FileName
151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.5.1.20151027.152735.1oe820t.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName 151027_RMD057
Date and time
StudyDate 20151027
StudyTime 152735.343000
SeriesTime 153542.390000
AcqTime 153336.015000
Acquisition parameters
PulseSeq tfl3d4_ns
Protocol T1_MEMPRAGE
PhEncDir ROW
EchoNo 1
FlipAngle 7
EchoTime 1.54
InversionTime 1100
RepetitionTime 2200
PhEncFOV 230
ReadoutFOV 230
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 192
NImageCols 192
NFrames 1
SliceArraylSize 1
IsMosaic 0
ImgPos 90.5719 127.9491 99.4836
VolRes 1.1979 1.1979 1.2000
VolDim 192 192 144
Vc 0.0126 -0.9958 -0.0903
Vr -0.0730 0.0892 -0.9933
Vs -0.9973 -0.0191 0.0716
VolCenter -2.5393 22.0298 -18.9494
TransferSyntaxUID 1.2.840.10008.1.2.4.90
UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault
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MGH-NMR Center
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