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.dcm 30100000-27.dcm

30100000-1.dcm 30100000-28.dcm

30100000-10.dcm 30100000-29.dcm

30100000-100.dcm 30100000-3.dcm

30100000-101.dcm 30100000-30.dcm

30100000-102.dcm 30100000-31.dcm

30100000-103.dcm 30100000-32.dcm

30100000-104.dcm 30100000-33.dcm

30100000-105.dcm 30100000-34.dcm

30100000-106.dcm 30100000-35.dcm

30100000-107.dcm 30100000-36.dcm

30100000-108.dcm 30100000-37.dcm

30100000-109.dcm 30100000-38.dcm

30100000-11.dcm 30100000-39.dcm

30100000-110.dcm 30100000-4.dcm

30100000-111.dcm 30100000-40.dcm

30100000-112.dcm 30100000-41.dcm

30100000-113.dcm 30100000-42.dcm

30100000-114.dcm 30100000-43.dcm

30100000-115.dcm 30100000-44.dcm

30100000-116.dcm 30100000-45.dcm

30100000-117.dcm 30100000-46.dcm

30100000-118.dcm 30100000-47.dcm

30100000-119.dcm 30100000-48.dcm

30100000-12.dcm 30100000-49.dcm

30100000-120.dcm 30100000-5.dcm

30100000-121.dcm 30100000-50.dcm

30100000-122.dcm 30100000-51.dcm

30100000-123.dcm 30100000-52.dcm

30100000-124.dcm 30100000-53.dcm

30100000-125.dcm 30100000-54.dcm

30100000-126.dcm 30100000-55.dcm

30100000-127.dcm 30100000-56.dcm

30100000-128.dcm 30100000-57.dcm

30100000-129.dcm 30100000-58.dcm

30100000-13.dcm 30100000-59.dcm

30100000-130.dcm 30100000-6.dcm

30100000-131.dcm 30100000-60.dcm

30100000-132.dcm 30100000-61.dcm

30100000-133.dcm 30100000-62.dcm

30100000-134.dcm 30100000-63.dcm

30100000-135.dcm 30100000-64.dcm

30100000-136.dcm 30100000-65.dcm

30100000-137.dcm 30100000-66.dcm

30100000-138.dcm 30100000-67.dcm

30100000-139.dcm 30100000-68.dcm

30100000-14.dcm 30100000-69.dcm

30100000-140.dcm 30100000-7.dcm

30100000-141.dcm 30100000-70.dcm

30100000-142.dcm 30100000-71.dcm

30100000-143.dcm 30100000-72.dcm

30100000-144.dcm 30100000-73.dcm

30100000-145.dcm 30100000-74.dcm

30100000-146.dcm 30100000-75.dcm

30100000-147.dcm 30100000-76.dcm

30100000-148.dcm 30100000-77.dcm

30100000-149.dcm 30100000-78.dcm

30100000-15.dcm 30100000-79.dcm

30100000-150.dcm 30100000-8.dcm

30100000-151.dcm 30100000-80.dcm

30100000-152.dcm 30100000-81.dcm

30100000-153.dcm 30100000-82.dcm

30100000-154.dcm 30100000-83.dcm

30100000-155.dcm 30100000-84.dcm

30100000-156.dcm 30100000-85.dcm

30100000-157.dcm 30100000-86.dcm

30100000-158.dcm 30100000-87.dcm

30100000-159.dcm 30100000-88.dcm

30100000-16.dcm 30100000-89.dcm

30100000-160.dcm 30100000-9.dcm

30100000-17.dcm 30100000-90.dcm

30100000-18.dcm 30100000-91.dcm

30100000-19.dcm 30100000-92.dcm

30100000-2.dcm 30100000-93.dcm

30100000-20.dcm 30100000-94.dcm

30100000-21.dcm 30100000-95.dcm

30100000-22.dcm 30100000-96.dcm

30100000-23.dcm 30100000-97.dcm

30100000-24.dcm 30100000-98.dcm

30100000-25.dcm 30100000-99.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

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





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