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
___
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
gr...@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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
