Hi Douglas, it looks like there is something wrong with those dicom files because they are missing some key information. Where did they come from? Did you anonymize them? doug

On 2/5/14 10:05 AM, Douglas Wojcik wrote:

Good morning;

I am new to freesurfer, and I am having issues getting my dataset imported; Any help will

be greatly appreciated;

I am running:

[root@satellite cd_files]# uname -a Linux satellite 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

I have copied the dicom files into the following directories:

[root@satellite cd_files]#pwd /opt/local/freesurfer/subjects/cd_files [root@satellite cd_files]# ls Autorun.inf Cache DICOM DICOMDIR Reports Viewer ViewImages.cmd

I try to import the images, & and it looks like it is missing some metadata:

[root@satellite freesurfer]# recon-all -s 20442 -i /opt/local/freesurfer/subjects/cd_files/DICOMDIR Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /opt/local/freesurfer/subjects Actual FREESURFER_HOME /opt/local/freesurfer Linux satellite 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /opt/local/freesurfer/subjects/20442

mri_convert /opt/local/freesurfer/subjects/cd_files/DICOMDIR /opt/local/freesurfer/subjects/20442/mri/orig/001.mgz

mri_convert /opt/local/freesurfer/subjects/cd_files/DICOMDIR /opt/local/freesurfer/subjects/20442/mri/orig/001.mgz WARNING: searching dicom file /opt/local/freesurfer/subjects/cd_files/DICOMDIR for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /opt/local/freesurfer/subjects/cd_files/DICOMDIR... WARNING: searching dicom file /opt/local/freesurfer/subjects/cd_files/DICOMDIR for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. Starting DICOMRead2() dcmfile = /opt/local/freesurfer/subjects/cd_files/DICOMDIR dcmdir = /opt/local/freesurfer/subjects/cd_files WARNING: tag ImageNumber not found in /opt/local/freesurfer/subjects/cd_files/DICOMDIR WARNING: tag SeriesNumber not found in /opt/local/freesurfer/subjects/cd_files/DICOMDIR WARNING: tag image orientation not found in /opt/local/freesurfer/subjects/cd_files/DICOMDIR Ref Series No = 21729 ERROR: bits = 0 not supported. Send email to freesurfer@nmr.mgh.harvard.edu Linux satellite 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 20442 exited with ERRORS at Wed Feb 5 08:50:54 CST 2014

For more details, see the log file /opt/local/freesurfer/subjects/20442/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I don't know that this is a bug, or just a low-compliance set of dicom files; Unable to find a similiar issue in the archives...

Any suggestions would be greatly appreciated, and Many Thanks in Advance;

Douglas

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