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BIC-MNI / minc-toolkit

Metaproject uniting all the available minc tools
GNU General Public License v3.0
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itk_convert (from EZminc) ignores space units #38

Open mcvaneede opened 8 years ago

mcvaneede commented 8 years ago

This is not truly specific to the minc-toolkit, but issues for EZminc have been disabled, and I'd like to keep a record just in case.

When you run itk_convert on an nrrd file to convert it to MINC, it assumes that the space directions (which contain the resolution) are set in mm. There's a attribute in the nrrd header that specifies the space units which for instance can be set to inch. In that case, the resolution for the output MINC file will be incorrect.

vfonov commented 8 years ago

Does ITK interpret these flags correctly?

mcvaneede commented 8 years ago

I'm not sure, don't actually work with ITK all that often. What's the best way to check?

vfonov commented 8 years ago

open in ITK-SNAP? itk_convert doesn't know much about file formats - it reads and writes whatever ITK can read and write.

mcvaneede commented 8 years ago

Ah, no, itksnap also ignores the space units. In that case it's just good to keep in mind that you might have to run minc_modify_header on the MINC output when the space units of the nrrd file are not given in mm.