general-discussion > NIAK and Windows.
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Nov 22, 2011  06:11 AM | Mouna S.
NIAK and Windows.
Dear Pierre, I am using NIAK- with Matlab R2007b on a Windows PC. I am having problems with reading/writing MINC files. I get the following error in Matlab:"??? Error using ==> niak_read_hdr_minc at 96niak:read: Could not parse the minc header !" I understand NIAK is optimised for Linux, so I wodner if my problem is due to the Windows O/S.  Thanks, - Mouna
Nov 27, 2011  12:11 PM | Pierre Bellec
RE: NIAK and Windows.
Dear Mouna,

Sorry for the late answer. I never managed to have NIAK run on Windows. Unfortunately, so far the simplest option you have is to install a virtual machine to run Ubuntu from windows. I'd recommend the fantastic neurodebian (http://neuro.debian.repository that comes with a large number of preconfigured packages (including minc). Not all the tools necessary to use NIAK come with neurodebian, but there is enough to read/write minc. You can compile the whole minc bundle easily on ubuntu (instructions here I have started a small project that may work for you if you only need to read minc. It is using the native HDF5 libraries of Matlab, and does not require any additional software (i.e. it will work without an install of the Minc tools).

This is an on-going (half finished) project, and you will need to pull out the code directly from the subversion repository. But in most cases the reader works fine. In the long term it will be more robust than the current MINC reader/writer implemented in NIAK.

I hope this helps. Best regards,

Nov 30, 2011  08:11 PM | Yaroslav Halchenko
RE: NIAK and Windows.
thank you for your kind feedback about NeuroDebian ;-) 

If you are interested -- we could help out with packaging NIAK (and corresponding dependencies) for Debian.  Unfortunately ourselves we do not have resources ATM to take care about packaging ourselves but would be glad to help out, mentor, and sponsor uploads into (Neuro)Debian.  The only obvious licensing problem I saw is wavelab -- have you contacted by any chance the authors regarding licensing?

In any case -- keep on good work, and if willing to take care about packaging, drop us a note (

Dec 4, 2011  11:12 AM | Pierre Bellec
RE: NIAK and Windows.
Dear Yaroslav,

I clearly am interested. NIAK has two dependencies : octave and the minc "bundle" (which includes the minc tools and a few additional packages). The main blocker is the MINC bundle, but I believe that Andrew Janke is working towards expanding the set of MINC tools available in Neurodebian. I'm going to check with him what his timeline is. Also, thanks for reminding me about the WaveLab license, we need to sort that out asap. I'll contact you when we start looking into the packaging.

Best regards,

Dec 8, 2011  04:12 PM | Yaroslav Halchenko
RE: NIAK and Windows.
Sounds like a plan.  Feel welcome to join neurodebian-devel mailing list to ask questions/seek advice (that is where we had recent dialog with Andrew Janke and got ourselves 1 more mirror ;) )