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/> 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/>
Linux 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