[MINC-users] the future of MINC and MINC support - need 2 min.

[Andrew Janke]

Hi Louis,

No, I don't use MINC anymore. But then I'm now on the professional side of
Uni's. I can say that in the two Oz based Uni's (Uni of Sydney and
Queensland Uni of Technology) that I've worked in, both have MINC in their
list of pre-compiled packages for the HPC.  I suspect there are many users
of MINC who aren't aware of it, an example freesurfer at times had a
clandestine MINC package included. That always was one of our MINC goals.

The last time I was an academic (7 years ago) I did use MINC extensively
for pre-clinical imaging and materials imaging. (rocks, fish, uCT, etc).
The functional gap that MINC fills that no other tools could was the
"doesn't look like an fMRI experiment" data. Sparse sampling, non-standard
axes, very large datasets that didn't fit in RAM. Perhaps over time
this functional gap has been filled with others.

When I was developing/maintaining MINC the most soul-crushing task was
keeping converters up to date. You knew you had to do it, but you knew that
it was all throw-away work as manufacturers would continue to change and in
the back of your mind you were always worried about preserving historic
behaviour. The reason to keep up the effort was preservation of meta-data
that didn't survive the X -> Nifti/BIDS -> MINC conversion.

So, if conversion is the barrier as it seems now, I'd back John Sled's
comment, if the conversion is sufficiently lossless you could reduce the
maintenance effort substantially by picking a winner format and focus
effort on a bi-directional converter?

All good things do eventually come to an end, perhaps this is the next
evolution of MINC? In my time it was netCDF -> HDF5 when netCDF support was
abandoned.

Thanks

a


On Tue, 27 May 2025 at 00:23, Louis Collins, Mr <louis.collins at mcgill.ca>
wrote:

> Hi all,
>
> I’m sending this email to bic-annouce, minc-users and minc-developers.
> Forgive me if you get multiple similar copies, each one has different
> questions addressed to the specific mailing list audience.
>
> Along with cutting edge neuro-imaging devices, the MINC software tools are
> an integral part of the success that have enabled the BIC to achieve
> world-wide recognition in neuroscience.  Unfortunately, a recent DICOM to
> MINC conversion issue (left-right flipping in MRI) has called into question
> the future of minc.
>
> The minc file format, API, and all image analysis pipelines have been
> supported mostly on a volunteer basis for at least the past decade.  While
> I’ve never had grants to support minc directly, I’ve used funds from other
> projects to support Vlad’s salary as he spent half his time to work on minc
> tools as we needed them in my lab.  We’ve also invested a lot of time (and
> $$) fixing bugs and assisting other groups with their processing needs.
> Mallar, Jason, Andrew and others have done the same.  At this time, my
> grants are running out, and I can no longer afford to support minc as we’ve
> done in the past. for a few months last fall, Julien provided some
> financial help (20% of an FTE), but that aid ended early this year.
>
> I learned about this new dcm2mnc issue last week that affects all those
> that use Seimens MRI data in minc format acquired in the past few months.
>
> This issue calls into the question the sufficiency of volunteer MNC
> support. Some have suggested to drop MINC altogether and to use other tools
> based on nifti/BIDS.  I believe that MINC support requires specific funding.
>
>
> For everyone in the minc-users list,  I am curious to know how many people
> are using MINC at present.
>
> Please respond with “YES - I’m using MINC” (or "no, not using MINC”).
> If YES, please also say if you’d like to continue using minc.
> If no, would you use minc if it was supported/documented?
>
> Feel free to reply all in this mailing list, or directly to me by email.
>
> my goal is to get a count of those using minc tools as soon as possible.
> there is a meeting this week to discuss the future of minc.
>
> thanks.
>
> -Louis
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>