[MINC-users] MINC support in Brainstorm

[François Tadel]

Dear colleagues,

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:
http://neuroimage.usc.edu/brainstorm
http://neuroimage.usc.edu/brainstorm/Screenshots
http://neuroimage.usc.edu/brainstorm/Community

It is already widely used in the world and supports natively many file 
formats for all sorts of data types. As we use the individual anatomy of 
the subjects/patients to estimate and visualize the cortical activity, 
we provide a variety of user-friendly tools for displaying and 
manipulating MRI volumes and surfaces.

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. This works as a temporary 
solution, but leads to a few questions:

1) There is no current distribution of mnc2nii for Windows systems. I 
found an old one on a website (I didn't keep track of where), but that 
is probably outdated:

    program: 2.0.15
    libminc: 2.0.15
    netcdf : 3.5.0
    HDF5   : 1.6.7

=> Is there a way to get a new build (and regular updates) of this 
program for Windows systems?
=> Can we re-distribute this Windows version of mnc2nii as part of the 
main distribution of Brainstorm?

2) The mnc2nii solution is not going to be a valid long-term solution 
for one specific reason: the import of the CIVET output surfaces in 
Brainstorm.
By converting to NIfTI, we lose the initial MINC coordinate system, on 
which all the CIVET output is based. If I don't have access to the 
origin of the referential, I don't think I can register correctly the 
cortical envelopes generated by CIVET with the corresponding T1 MRI.
Therefore we will need a different solution for importing the MINC volumes.

3) Since HDF5 and netCDF are formats that are fully supported in many 
platform-independent languages (Java, Matlab, Python), will there be at 
some point a MINC reader available that does not rely on any external 
compiled library?
I looked at Pierre Bellec's Matlab functions 
(http://code.google.com/p/mominc/), but for what I understood it does 
the reading of the HDF5/netCDF contents and does not provide any tool to 
re-orient the the volume in another standard coordinate system (such as 
NIfTI).
There is probably not much to add to get a Matlab-based (or Java-based) 
version of mnc2nii (that reads the MINC volume into a NIfTI-oriented 
volume but with the full MINC header information).
Are there other solutions readily available to help us with this MINC 
import?
Is anybody working on or interested in those aspects at the present time?

Those would be very helpful tools for us and probably for the developers 
of other software packages as well. We would be willing to help for any 
new developments in this direction, and more generally support the 
integration between the different software environments at the Neuro.

Thanks
Francois



-- 
François Tadel, MSc
MEG / McConnell Brain Imaging Center / MNI / McGill University
3801 rue University, Montreal, QC H3A2B4, Canada