Hi, I've been trying to sort some dicom and to convert them into nifti volumes. I am using the command:
unpacksdcmdir -src $source -targ $target -fsfast -scanonly series.txt
but the process gives me this error: Log file created by unpacksdcmdir $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $ /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/unpack.log /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI Thu Aug 16 15:27:30 EDT 2012 -src /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM -targ /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI -fsfast -scanonly series.txt mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/16-19:27:30-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400 FreeSurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux SkipMoCo 0 dicomdir /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM Scanning source directory ... INFO: summary file is /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/dicomdir.sumfile INFO: status file is /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/parse.status mri_parse_sdcmdir --sortbyrun --d /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM --o /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/dicomdir.sumfile --status /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/parse.status INFO: scanning path to Siemens DICOM DIR: /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM INFO: Found 2054 files in /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM INFO: counting Siemens Files $Id: mri_parse_sdcmdir.c,v 1.21 2011/03/02 00:04:23 nicks Exp $ cwd /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI cmdline --sortbyrun --d /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM --o /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/dicomdir.sumfile --status /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/parse.status
sysname Linux hostname FreeSurfer machine i686 user virtualuser INFO: found 0 Siemens Files ERROR: scanning directory /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM Done scanning Thu Aug 16 15:35:00 EDT 2012 ------------------------------------------ ERROR: no dicom files found in /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM
Then I decided to use directly MRI_convert with a random first_dicom_file just to understand better what was the problem and the process gives me a new error:
mri_convert DICOM/IM_0002.dcm prova.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from DICOM/IM_0002.dcm... Starting DICOMRead2() dcmfile = DICOM/IM_0002.dcm dcmdir = DICOM Ref Series No = 301 Found 2055 files, checking for dicoms WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found Found 351 dicom files in series. WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: 89.4924 -139.133 124.026 Vs: 0.432834 -0.672923 0.599858 Second Sorting Counting frames nframes = 1 nslices = 351 ndcmfiles = 351 MRIalloc(0, 0, 351): bad parm No such file or directory ERROR: mri alloc failed
I saw that other people had a similar problem in the past: my images come from a Philips Achieva 3T, and this is probably the problem (or I am doing something wrong). However I did not find any solution in the old threads of the mailing list. I can send one dicom file if this can help. Thank you Maria