You can look at the help (dcmupack -help) for info, but basically you run it twice. First dcmunpack -src dicomdir This will give you a list of runs, then run it specifying the runs that you want to unpack. It takes the same command line options as unpacksdcmdir doug
On 08/20/2012 10:05 AM, Alexandra Tanner wrote:
Hi Doug,
Thanks! Do you know what command line I should use with dcmunpack? I can't specify the run number since I don't currently have that information for my scan, only the DICOM files. Typically when we unpack our Siemens files we use the following command line: "unpacksdcmdir -src<source> -targ <target> -run<last MEMPRAGE scan> MPRAGE COR blah" -- for this scan should I be converting to mgh/mgz instead?
Thanks, Alex
dcmunpack will convert them to whatever file format you want (don't use COR though). doug
On 08/20/2012 09:51 AM, Alexandra Tanner wrote:
Thanks Bruce. I see that because these are not Siemens scans I need to use the command dcmunpack instead of unpacksdcmdir, however, if the DICOM files are already saved on our cluster do the files need to be unpacked or simply converted to COR format using mri_convert? Thanks!
Best, Alex
Hi Alex The dicoms should be enough Bruce
On Aug 16, 2012, at 4:10 PM, "Alexandra Tanner" atanner@nmr.mgh.harvard.edu wrote:
Dear Doug,
We're getting T1 DICOM files from the Clinical PACS System (via mi2b2) and would like to pull them info the freesurfer stream to get cortical thickness. In order to run the standard unpacking commands, do we need any other files besides the DICOM files themselves? Of note, these scans were acquired on a variety of clinical scanners at MGH. Any suggestions you have would be greatly appreciated!
Thanks, Alex _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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