| T O P I C R E V I E W |
| dvsmith |
Posted - Jan 15 2010 : 11:07:59 AM
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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| 8 L A T E S T R E P L I E S (Newest First) |
| dvsmith |
Posted - Jan 23 2010 : 12:54:08 PM
thanks, Chris! |
| petty |
Posted - Jan 22 2010 : 3:15:06 PM
actually i just stuck it on all the current nodes as well. |
| petty |
Posted - Jan 22 2010 : 2:45:56 PM
it'll be on the new cluster |
| dvsmith |
Posted - Jan 15 2010 : 5:47:10 PM
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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| syam.gadde |
Posted - Jan 15 2010 : 1:08:26 PM
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 |
Posted - Jan 15 2010 : 1:03:49 PM
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! |
| dvsmith |
Posted - Jan 15 2010 : 12:48:49 PM
I use the BXH tools for BIAC data... But I have other data that is not from BIAC. |
| petty |
Posted - Jan 15 2010 : 11:26:15 AM
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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