Thanks for your help, Doug. Here's what I get when I run mri_convert on its own:
mri_convert 151027_RMD057/RAW//151027_RMD057.MR.INVESTIGATORS_Dillon.5.1.20151027.152735.1oe820t.dcm 151027_RMD057/3danat/005/T1.nii --sdcmlist 151027_RMD057/3danat/005/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from 151027_RMD057/RAW//151027_RMD057.MR.INVESTIGATORS_Dillon.5.1.20151027.152735.1oe820t.dcm... INFO: found 144 files in list file INFO: loading series header info. INFO: sorting. RunNo = 4 INFO: (192 192 144), nframes = 1, ismosaic=0 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 Segmentation fault Dan On May 11, 2017, at 12:13 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> wrote: 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><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><http://ncfc22.rc.fas.harvard.edu/> Linux ncfc22.rc.fas.harvard.edu<http://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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