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dvsmith
Advanced Member
USA
218 Posts |
 Posted - Jan 15 2010 : 11:07:59 AM
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Hi,
Could we install dcm2nii on the cluster nodes? I suspect it would be easy to install, and it would be very helpful for anyone working with DICOM images.
http://www.cabiatl.com/mricro/mricron/dcm2nii.html
It would definitely need to be periodically updated to keep up with the latest releases and image formats.
Thanks!
David
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petty
BIAC Staff
USA
453 Posts |
Posted - Jan 15 2010 : 11:26:15 AM
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if you're using data from BIAC then you could just convert with the bxh-tools which are already installed, since all data comes with bxh headers.
bxh2analyze --niigz -s DCMINPUT.bxh OUTPUT
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dvsmith
Advanced Member
USA
218 Posts |
Posted - Jan 15 2010 : 12:48:49 PM
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| I use the BXH tools for BIAC data... But I have other data that is not from BIAC. |
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dvsmith
Advanced Member
USA
218 Posts |
Posted - Jan 15 2010 : 1:03:49 PM
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If it's easier, how could I do this myself? Just ssh into every node and dump it into my home directory? The BXH file format is very specialized, and one generally encounters DICOM format at most other sites -- which is sometimes the format of data downloaded from the FMRI data center.
Thanks! |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jan 15 2010 : 1:08:26 PM
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As an alternative, you could run dicom2bxh and then run bxh2analyze. There may be other reasons you wish to use dcm2nii of course, but if the only reason is to get to NIFTI, we've used the following commands on innumerable datasets:
dicom2bxh *.dcm tmp.bxh
bxh2analyze --niigz tmp.bxh OUTPUTPREFIX
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dvsmith
Advanced Member
USA
218 Posts |
Posted - Jan 15 2010 : 5:47:10 PM
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Thanks, Syam... I think dcm2nii is better suited to my current needs, so I'll either use that locally or dump it in my home directory on each node so that I can make use of the cluster. It's standalone, so it should work fine...
Cheers,
David
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petty
BIAC Staff
USA
453 Posts |
Posted - Jan 22 2010 : 2:45:56 PM
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| it'll be on the new cluster |
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petty
BIAC Staff
USA
453 Posts |
Posted - Jan 22 2010 : 3:15:06 PM
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| actually i just stuck it on all the current nodes as well. |
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dvsmith
Advanced Member
USA
218 Posts |
Posted - Jan 23 2010 : 12:54:08 PM
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| thanks, Chris! |
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Topic |
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installing dcm2nii?
