Hi
i work on the BIC servers on a linux machine

When i tried to use the demo function and datasets included in the NIAK 0.6.3 minc function seems not to works with mincV2 images.
Moreover the templates included in the package are in minc v2 so some brick function does not works.

MINC package is installed on our servers, maybe there are outdated ?


best regards
Alexis

Dear Alexis,

Thanks for reporting that issue. What's happening is that you are using the MINC1 package, which is the default at the BIC and does not support the MINC2 file format. The MINC2 package is also installed though, and does support both MINC1 and MINC2 formats (note the subtle difference between MINC2 package and format). NIAK works with both MINC1 and MINC2 file formats, but was written with the lattest version of the MINC tools, i.e. MINC 2.+. I don't think that the MINC1 package is being actively developed anymore. To use the MINC2 package at the BIC, you simply need to change the search path of your terminal. The method is different if you are using a bash or a csh terminal.

If you are using bash, edit the file .bashrc in your home directory and add the following line :
export PATH=/usr/local/bic/bin:$PATH

Note that the MINC2 package will force the outputs to be in MINC2. If you want to keep using the MINC1 format, you have to unset this behavior by adding an additional line:
unset MINC_FORCE_V2

If you are using csh, edit the file .cshrc in your home directory and add the following line :
set path = (/usr/local/bic/bin $path)

To keep using MINC1, the line is then :
unsetenv MINC_FORCE_V2

One final comment : this won't happen if you're using a pipeline. The pipeline manager has been configured at the BIC to use the MINC2 package, and this is transparent for users. I hope this will solve your issue. Best regards,

Pierre

Thanks a lot it seems to work now