It looks like there is a lot of information missing from the dicom file. Did it come directly from the scanner? Or was it transformed in some way? Anonymized?
On 2/4/16 5:06 PM, Kan Ding wrote:
Hi, I am having trouble to generate .mgz file from DICOM. However, I was able to run the same code with NIFTI file. What did I do wrong? Thanks for your help. Kan
NUA502608:300T1 kding$ ls
30100000-0.dcm30100000-27.dcm
30100000-1.dcm30100000-28.dcm
30100000-10.dcm30100000-29.dcm
30100000-100.dcm30100000-3.dcm
30100000-101.dcm30100000-30.dcm
30100000-102.dcm30100000-31.dcm
30100000-103.dcm30100000-32.dcm
30100000-104.dcm30100000-33.dcm
30100000-105.dcm30100000-34.dcm
30100000-106.dcm30100000-35.dcm
30100000-107.dcm30100000-36.dcm
30100000-108.dcm30100000-37.dcm
30100000-109.dcm30100000-38.dcm
30100000-11.dcm30100000-39.dcm
30100000-110.dcm30100000-4.dcm
30100000-111.dcm30100000-40.dcm
30100000-112.dcm30100000-41.dcm
30100000-113.dcm30100000-42.dcm
30100000-114.dcm30100000-43.dcm
30100000-115.dcm30100000-44.dcm
30100000-116.dcm30100000-45.dcm
30100000-117.dcm30100000-46.dcm
30100000-118.dcm30100000-47.dcm
30100000-119.dcm30100000-48.dcm
30100000-12.dcm30100000-49.dcm
30100000-120.dcm30100000-5.dcm
30100000-121.dcm30100000-50.dcm
30100000-122.dcm30100000-51.dcm
30100000-123.dcm30100000-52.dcm
30100000-124.dcm30100000-53.dcm
30100000-125.dcm30100000-54.dcm
30100000-126.dcm30100000-55.dcm
30100000-127.dcm30100000-56.dcm
30100000-128.dcm30100000-57.dcm
30100000-129.dcm30100000-58.dcm
30100000-13.dcm30100000-59.dcm
30100000-130.dcm30100000-6.dcm
30100000-131.dcm30100000-60.dcm
30100000-132.dcm30100000-61.dcm
30100000-133.dcm30100000-62.dcm
30100000-134.dcm30100000-63.dcm
30100000-135.dcm30100000-64.dcm
30100000-136.dcm30100000-65.dcm
30100000-137.dcm30100000-66.dcm
30100000-138.dcm30100000-67.dcm
30100000-139.dcm30100000-68.dcm
30100000-14.dcm30100000-69.dcm
30100000-140.dcm30100000-7.dcm
30100000-141.dcm30100000-70.dcm
30100000-142.dcm30100000-71.dcm
30100000-143.dcm30100000-72.dcm
30100000-144.dcm30100000-73.dcm
30100000-145.dcm30100000-74.dcm
30100000-146.dcm30100000-75.dcm
30100000-147.dcm30100000-76.dcm
30100000-148.dcm30100000-77.dcm
30100000-149.dcm30100000-78.dcm
30100000-15.dcm30100000-79.dcm
30100000-150.dcm30100000-8.dcm
30100000-151.dcm30100000-80.dcm
30100000-152.dcm30100000-81.dcm
30100000-153.dcm30100000-82.dcm
30100000-154.dcm30100000-83.dcm
30100000-155.dcm30100000-84.dcm
30100000-156.dcm30100000-85.dcm
30100000-157.dcm30100000-86.dcm
30100000-158.dcm30100000-87.dcm
30100000-159.dcm30100000-88.dcm
30100000-16.dcm30100000-89.dcm
30100000-160.dcm30100000-9.dcm
30100000-17.dcm30100000-90.dcm
30100000-18.dcm30100000-91.dcm
30100000-19.dcm30100000-92.dcm
30100000-2.dcm30100000-93.dcm
30100000-20.dcm30100000-94.dcm
30100000-21.dcm30100000-95.dcm
30100000-22.dcm30100000-96.dcm
30100000-23.dcm30100000-97.dcm
30100000-24.dcm30100000-98.dcm
30100000-25.dcm30100000-99.dcm
30100000-26.dcm
NUA502608:300T1 kding$ recon-all -i 30100000-0.dcm -s 300
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Users/kding/desktop/data/TBIE/TBIET1/300T1
Actual FREESURFER_HOME /Applications/freesurfer
Darwin nua502608.dhcp.swmed.org 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
/Users/kding/desktop/data/TBIE/TBIET1/300T1/300
\n mri_convert /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm /Users/kding/desktop/data/TBIE/TBIET1/300T1/300/mri/orig/001.mgz \n
mri_convert /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm /Users/kding/desktop/data/TBIE/TBIET1/300T1/300/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm...
Starting DICOMRead2()
dcmfile = /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm
dcmdir = /Users/kding/desktop/data/TBIE/TBIET1/300T1
WARNING: tag ImageNumber not found in /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm
WARNING: tag image orientation not found in /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm
Ref Series No = 18976
ERROR: bits = 0 not supported.
Send email to freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Darwin nua502608.dhcp.swmed.org 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
recon-all -s 300 exited with ERRORS at Thu Feb 4 15:53:19 CST 2016
For more details, see the log file /Users/kding/desktop/data/TBIE/TBIET1/300T1/300/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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