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

Thu May 29 04:29:00 EDT 2025

Hi Louis,

Yes, our team at the A.I. Virtanen Institute in Finland has been using MINC
and minc-toolkit for processing ex vivo MRI and histology datasets since
2023 - and will continue to do so for the next 2-3 years at least.
Thanks for all the volunteer work that has gone into developing and
supporting these tools.

Best,

Mastaneh Torkamani

Postdoctoral Researcher
Biomedical Image Analysis Group
A.I. Virtanen Institute for Molecular Sciences
University of Eastern Finland
https://www.linkedin.com/in/mastaneh-torkamani-azar/

On Mon, May 26, 2025 at 7:00 PM <minc-users-request at bic.mni.mcgill.ca>
wrote:

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> Today's Topics:
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>    1. the future of MINC and MINC support - need 2 min.
>       (Louis Collins, Mr)
>    2. Re: the future of MINC and MINC support - need 2 min.
>       (Simone Zehntner)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 26 May 2025 14:19:28 +0000
> From: "Louis Collins, Mr" <louis.collins at mcgill.ca>
> To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] the future of MINC and MINC support - need 2
>         min.
> Message-ID: <E2138E13-F1C2-4991-860B-7C2742967774 at mcgill.ca>
> Content-Type: text/plain; charset="utf-8"
>
> 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
>
> ------------------------------
>
> Message: 2
> Date: Mon, 26 May 2025 11:32:16 -0400
> From: Simone Zehntner <simone at biospective.com>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] the future of MINC and MINC support - need 2
>         min.
> Message-ID:
>         <
> CANrx1iPHSxwyARPJ4jdYBxhUcZOQBDUUmKM26ra6uYkxE8-dwA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> YES - I?m using MINC
> I would like to continue using MINC
>
> -Simone
>
> On Mon, May 26, 2025 at 10:23?AM 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
> >
>
>
> ------------------------------
>
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> ------------------------------
>
> End of MINC-users Digest, Vol 177, Issue 1
> ******************************************
>