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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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