Error with recon-all import step. ERROR: the pixel data cannot be loaded as it is JPEG compressed.
I am trying to import an MPRAGE structural sequence of 160 images acquired from a Siemens Allegro. Only one of my subjects displays the following error message when I try to import him using the "recon-all -s Subject -i" function. Below is the brief error message and full log. Thanks in advance for any assistance.
*ERROR: the pixel data cannot be loaded as it is JPEG compressed.*
Full Log Below: [Jill:freesurfer/subjects/RawDicoms] lab% recon-all -s SZ0069TS -i SZ0069TS/IM-0001-441581576-0001.dcm Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 /Applications/freesurfer/subjects/SZ0069TS \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm... Getting Series No INFO: Found 163 files in /Applications/freesurfer/subjects/RawDicoms/SZ0069TS INFO: Scanning for Series Number 20 Scanning Directory INFO: found 160 files in series INFO: loading series header info.
RunNo = 19 INFO: sorting. INFO: (256 256 160), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 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) Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s SZ0069TS exited with ERRORS at Mon Jul 30 11:38:40 CDT 2012
For more details, see the log file /Applications/freesurfer/subjects/SZ0069TS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Take care, Nathan Hutcheson Graduate Research Assistant 501 Sparks Center 1748 7th Ave South Birmingham, AL 35233
it looks like someone accidentally turn on jpeg compression on the console. Our converter does not read jpeg. You can use dcmdjpeg from the dcmtk toolkit to create new dicoms that are uncompressed, something like
dcmdjpeg +te old.dcm new.dcm
doug
On 07/30/2012 01:00 PM, Nathan Hutcheson wrote:
I am trying to import an MPRAGE structural sequence of 160 images acquired from a Siemens Allegro. Only one of my subjects displays the following error message when I try to import him using the "recon-all -s Subject -i" function. Below is the brief error message and full log. Thanks in advance for any assistance.
*ERROR: the pixel data cannot be loaded as it is JPEG compressed.*
Full Log Below: [Jill:freesurfer/subjects/RawDicoms] lab% recon-all -s SZ0069TS -i SZ0069TS/IM-0001-441581576-0001.dcm Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 /Applications/freesurfer/subjects/SZ0069TS \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm... Getting Series No INFO: Found 163 files in /Applications/freesurfer/subjects/RawDicoms/SZ0069TS INFO: Scanning for Series Number 20 Scanning Directory INFO: found 160 files in series INFO: loading series header info.
RunNo = 19 INFO: sorting. INFO: (256 256 160), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 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) Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s SZ0069TS exited with ERRORS at Mon Jul 30 11:38:40 CDT 2012
For more details, see the log file /Applications/freesurfer/subjects/SZ0069TS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Take care, Nathan Hutcheson Graduate Research Assistant 501 Sparks Center 1748 7th Ave South Birmingham, AL 35233
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Douglas N Greve -
Nathan Hutcheson