From lconcha at unam.mx  Wed Jul  2 16:04:06 2025
From: lconcha at unam.mx (Luis Concha)
Date: Wed, 2 Jul 2025 14:04:06 -0600
Subject: [MINC-users] the future of MINC and MINC support - need 2 min.
In-Reply-To: <17381A89-0545-434D-B207-111EC51A51B8@rogue-research.com>
References: <E2138E13-F1C2-4991-860B-7C2742967774@mcgill.ca>
 <17381A89-0545-434D-B207-111EC51A51B8@rogue-research.com>
Message-ID: <CAOq9ZoF+7_GLbEBHj1aVezCyuZ9HjOk89MCQ9Kwa=73n2GNUBA@mail.gmail.com>

Hello and sorry for the late reply.

YES - I'm using MINC. We use it at the National Laboratory for MRI (Mexico)
for human and rodent studies, mainly using the tools developed at the
CobraLab (thanks!).

I cannot add much more to what others have already commented on. Despite
the fact that other image formats have become more widely adopted than mnc,
the overall minc ecosystem remains valid, useful, and in many aspects still
superior to other tools. I am saddened to hear that the future of minc is
uncertain.

Cheers,

Luis

Dr. Luis Concha
Instituto de Neurobiolog?a
Laboratorio C-13
UNAM, Campus Juriquilla
Boulervard Juriquilla 3001
Juriquilla, Quer?taro.
C.P. 76230
M?xico
Tel (442) 2 38 10 54
Fax (442) 2 38 10 46
http://personal.inb.unam.mx/lconcha/


On Fri, May 30, 2025 at 4:10?PM Sean McBride <sean at rogue-research.com>
wrote:

> Louis,
>
> YES - I?m using MINC
>
> Here at Rogue Research we support the MINC file format in our Brainsight
> application, mostly for MRI/CT images, anatomical and functional.
>
> Our app supports MINC1 files via the VTK library's vtkMINCImageReader
> class (which in turn uses NetCDF directly). We support MINC2 files via the
> ITK library's itk::MINCImageIO class (which in turn uses libMINC). We have
> contributed various patches to all this code over the years.
>
> Our app also supports other medical image file formats like DICOM, NIfTI,
> etc. We try to support any file a customer throws at us.
>
> Our app doesn't have any telemetry, so we don't really know how many of
> our users use which file formats.
>
> In addition, for some customers, we help them install the minc toolkit on
> their systems if they are looking to co-register MRI and CT of the same
> subject. For this we point them to the latest from here:
>
> https://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/?C=M;O=D
>
> Which I'm just now realizing (I think) does not actually have the latest,
> which is only in github?
>
> We'd like to continue using MINC. We'd be willing to contribute a little
> bit of money to a pot, if such a thing is set up.
>
> Cheers,
>
> Sean
> Rogue Research Inc.
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From gdevenyi at gmail.com  Mon Jul 14 12:49:47 2025
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Mon, 14 Jul 2025 12:49:47 -0400
Subject: [MINC-users] Announce: bids2mnc -- MINC as a derivative of BIDS
 datasets
Message-ID: <CAFQOoOo9dyyOJOefWpQJeX866FPKLVV7UmLHET9azJA=fHHcfQ@mail.gmail.com>

Hi all,

In my small contribution to keep the MINC ecosystem alive, while playing
nice with other major projects in neuroimaging, I'm happy to announce
bids2mnc.

https://github.com/CoBrALab/bids2mnc

The bids2mnc package takes an existing BIDS structured dataset and makes a
MINCified variant of it as a "BIDS derivative". MINC files have all of the
BIDS-standard metadata inserted in their header under a bids top-level tag.

It relies upon, nii2mnc, jq, and https://github.com/CoBrALab/libBIDS.sh to
have minimal (additional) dependencies for someone already using MINC.

Potential use cases here are:
- bypassing the current DICOM to MINC challenges with "enhanced DICOMS"
relying on the implementation in dcm2niix used for NIFTI conversion
- Generating MINC files from publicly available BIDS datasets

We hope users find it helpful in keeping MINC alive in their existing
workflows.

Contributions/questions/bugs always welcome at the Github. Thanks!


--
Gabriel A. Devenyi Ph.D.
gdevenyi at gmail.com