[MINC-users] MINC support in Brainstorm

[Andrew Janke]

Hi François

On 23 July 2013 02:09, François Tadel <francois.tadel at mcgill.ca> wrote:
> At the McGill MEG lab, we develop and support an open-source
> Matlab/Java-based environment for MEG/EEG/sEEG/ECOG processing and source
> reconstruction named Brainstorm:
>
> To open this analysis platform to the users at the Neuro, we are working on
> adding an easy support of the .mnc format for structural T1-weighted volumes
> in Brainstorm. For now, we are using mnc2nii to convert the volumes to a
> NIfTI format before reading them.

mnc2nii does output the co-ordinate information to the nii file but
there are a few ways of interpreting this, are you using niftilib to
import into your software?  If so it has been on my "list of things to
do one day" to update mnc2nii to use this at which point this problem
should go away.

Another option is to take advantage of the work that Vladimir has done
with ITK and minc integration. While a "heavier" solution it will
allow you to read in many other imaging formats as well with very
little work. There is also a "lite" version of MINC that works with
ITK that only requires HDF.

So, you have a choice, look into itk or I can work with someone in
your group to get mnc2nii up to scratch for what you need.

Thanks


a