Dear Freesurfer developers and users,
I experience error converting .dcm to .nii with mri_convert these days. I do not know why because it is not reproducible and error occurs mostly with new scans (MPRAGE and other functional sequences) from a Siemens Trio Tim 3T. Here is a display output as an example when I type : mri_convert IM-0001-0001.dcm anat.nii
mri_convert IM-0001-0001.dcm anat.nii $Id: mri_convert.c,v 1.171 2010/09/14 21:03:12 greve Exp $ reading from IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 106 files in /Users/dehaes/Work/Research/ASL/CHB/Data/Siemens_pasl/4503697/Anat INFO: Scanning for Series Number 5 INFO: found 104 files in series INFO: loading series header info.
INFO: sorting. RunNo = 4 INFO: (192 192 104), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 0.964 -0.234 -0.129 -6.753; 0.238 0.971 0.015 7.906; 0.122 -0.045 0.992 -5.687; 0.000 0.000 0.000 1.000;
ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70)
Does Siemens recently changes the way they write DICOM from the console? Do you guys know how to avoid this error?
Thanks Mathieu Dehaes
Hi Mathieu, I've never seen this before for pixel data. Sometimes people will draw something on an image in the console then save it as a dicom. Could this have happened with this data? Usually it's not 104 files though. doug
dehaes@nmr.mgh.harvard.edu wrote:
Dear Freesurfer developers and users,
I experience error converting .dcm to .nii with mri_convert these days. I do not know why because it is not reproducible and error occurs mostly with new scans (MPRAGE and other functional sequences) from a Siemens Trio Tim 3T. Here is a display output as an example when I type : mri_convert IM-0001-0001.dcm anat.nii
mri_convert IM-0001-0001.dcm anat.nii $Id: mri_convert.c,v 1.171 2010/09/14 21:03:12 greve Exp $ reading from IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 106 files in /Users/dehaes/Work/Research/ASL/CHB/Data/Siemens_pasl/4503697/Anat INFO: Scanning for Series Number 5 INFO: found 104 files in series INFO: loading series header info.
INFO: sorting. RunNo = 4 INFO: (192 192 104), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 0.964 -0.234 -0.129 -6.753; 0.238 0.971 0.015 7.906; 0.122 -0.045 0.992 -5.687; 0.000 0.000 0.000 1.000;
ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70)
Does Siemens recently changes the way they write DICOM from the console? Do you guys know how to avoid this error?
Thanks Mathieu Dehaes _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I visually checked all dcm files and nothing appeared as a mark or something else. The number of files is usually 176 but sometime 144 and 104. I do not know why but we work with newborn patients and I thought it could be related to the size of the FOV with respect to the size of the head. Otherwise, I only encounter this error a few times but the frequency increased since 2-3 weeks. Mathieu
-- Mathieu Dehaes, PhD Fetal-Neonatal Neuroimaging & Developmental Science Center Children's Hospital Boston - Department of Newborn Medicine Harvard Medical School - Department of Pediatrics
Children's Hospital Boston, 300 Longwood Ave, Boston, MA 02115 Tel: 857-218-5142, Fax: 617-730-4671
On Aug 30, 2011, at 12:15 PM, Douglas N Greve wrote:
Hi Mathieu, I've never seen this before for pixel data. Sometimes people will draw something on an image in the console then save it as a dicom. Could this have happened with this data? Usually it's not 104 files though. doug
dehaes@nmr.mgh.harvard.edu wrote:
Dear Freesurfer developers and users,
I experience error converting .dcm to .nii with mri_convert these days. I do not know why because it is not reproducible and error occurs mostly with new scans (MPRAGE and other functional sequences) from a Siemens Trio Tim 3T. Here is a display output as an example when I type : mri_convert IM-0001-0001.dcm anat.nii
mri_convert IM-0001-0001.dcm anat.nii $Id: mri_convert.c,v 1.171 2010/09/14 21:03:12 greve Exp $ reading from IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 106 files in /Users/dehaes/Work/Research/ASL/CHB/Data/Siemens_pasl/4503697/Anat INFO: Scanning for Series Number 5 INFO: found 104 files in series INFO: loading series header info.
INFO: sorting. RunNo = 4 INFO: (192 192 104), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 0.964 -0.234 -0.129 -6.753; 0.238 0.971 0.015 7.906; 0.122 -0.045 0.992 -5.687; 0.000 0.000 0.000 1.000;
ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70)
Does Siemens recently changes the way they write DICOM from the console? Do you guys know how to avoid this error?
Thanks Mathieu Dehaes _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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