Are these Siemens dicoms? If not, try dcmunpack doug

On 11/13/2014 01:06 PM, Shady El Damaty wrote:

Hi freesurfers,

I've been stuck on this problem for a while and couldn't find anything online to help me out so I've come to the mailing list as my last resort.

I am trying to unpack my functional data into fsl format using the unpacksdcmdir command. However, I am not successful using this command and get the error message: "no dicom files found"

This is the command I'm entering:

unpacksdcmdir -src $DICOMDIR -targ ~/Ultimatum/sess01 -scanonly Ultimatum-01_Import.log

When I list the contents of $DICOMDIR, I find that there are about 800 or so files with enumerated names ending in *.ACQ (e.g.: 1.ACQ, 2.ACQ... 800.ACQ).

Does anyone have any ideas why unpacksdcmdir isn't reading these files?

The output after running the command appears below.

Thanks in advance for your help!

Shady El Damaty

unpacksdcmdir -src $DICOMDIR -targ ~/Ultimatum/sess01 -scanonly Ultimatum-01_Import.log

$Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $

/glusterfs/mirror/cfmi/home/se394

-src /raw/dicom/data/cfmi/MR/2014/10/21/1.3.12.2.1107.5.2.32.35052.30000014101416403831200000052.STU/1.3.12.2.1107.5.2.32.35052.2014102112462587284871374.0.0.0.SER -targ /exports/home/se394/Ultimatum/sess01 -scanonly Ultimatum-01_Import.log

Thu Nov 13 12:59:20 EST 2014

mri_convert -all-info

ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/11/13-17:59:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: se394 Machine: node020.cfmi.georgetown.edu http://node020.cfmi.georgetown.edu Platform: Linux PlatformVersion: 3.10.0-123.9.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400

node020.cfmi.georgetown.edu http://node020.cfmi.georgetown.edu

Linux node020.cfmi.georgetown.edu http://node020.cfmi.georgetown.edu 3.10.0-123.9.2.el7.x86_64 #1 SMP Tue Oct 28 18:05:26 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Thu Nov 13 12:59:20 EST 2014

Log File is /exports/home/se394/Ultimatum/sess01/unpack.log

INFO: Logfile is /exports/home/se394/Ultimatum/sess01/unpack.log

SkipMoCo 0

Scanning source directory ...

INFO: summary file is /exports/home/se394/Ultimatum/sess01/dicomdir.sumfile

INFO: status file is /exports/home/se394/Ultimatum/sess01/parse.status

Scanning directory Thu Nov 13 12:59:20 EST 2014

mri_parse_sdcmdir --sortbyrun --d /raw/dicom/data/cfmi/MR/2014/10/21/1.3.12.2.1107.5.2.32.35052.30000014101416403831200000052.STU/1.3.12.2.1107.5.2.32.35052.2014102112462587284871374.0.0.0.SER --o /exports/home/se394/Ultimatum/sess01/dicomdir.sumfile --status /exports/home/se394/Ultimatum/sess01/parse.status

0

Done scanning Thu Nov 13 12:59:24 EST 2014

---

ERROR: no dicom files found in /raw/dicom/data/cfmi/MR/2014/10/21/1.3.12.2.1107.5.2.32.35052.30000014101416403831200000052.STU/1.3.12.2.1107.5.2.32.35052.2014102112462587284871374.0.0.0.SER

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