[MINC-users] MINC-users Digest, Vol 177, Issue 2

Tue May 27 09:43:42 EDT 2025

Hi Louis,

YES - I'm using MINC.

I am very grateful to you and everyone who maintains minc and makes it 
available. Thank you so much for volunteering your time on this, it has 
been a great resource for me.

Something that may (or may not) interest you is that I recently used 
minc to help someone with an art project: 
https://danielhoops.com/blog/2025/5/15/i-get-emails-art-for-brains-p7r37

Dan

On 27/5/25 22:16, minc-users-request at bic.mni.mcgill.ca wrote:
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> Today's Topics:
>
>     1. Re: the future of MINC and MINC support - need 2 min.
>        (Alex Zijdenbos)
>     2. Re: the future of MINC and MINC support - need 2 min.
>        (Christophe Grova, M)
>     3. Re: the future of MINC and MINC support - need 2 min.
>        (Khoo Hui Ming)
>     4. Re: the future of MINC and MINC support - need 2 min. (John Sled)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 26 May 2025 15:20:36 -0400
> From: Alex Zijdenbos <zijdenbos at gmail.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:
> 	<CABEEk15Be5PNSGUu1o6eBbjGFsFdwq4q1u+fjSWcUMFYHzxnNw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Louis,
>
> YES, using MINC, will continue to do so
>
> Are you able to elaborate on the L/R flipping issue? What the root cause
> is, what scanners/s/w version may be affected, etc? We have gone through a
> lot of Siemens data from different sites, cross-referencing it with a
> conversion via NifTI, and haven't found any unexpected flips (I should note
> that that is with our (Biospective in-house) version of dcm2mnc, that has
> diverged from the "standard" one).
>
> -- A
>
> 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
>>
>>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 27 May 2025 11:06:50 +0000
> From: "Christophe Grova, M" <christophe.grova at mcgill.ca>
> To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] the future of MINC and MINC support - need 2
> 	min.
> Message-ID:
> 	<YT3PR01MB9428D40A9C9B4185F7F2D17F9064A at YT3PR01MB9428.CANPRD01.PROD.OUTLOOK.COM>
> 	
> Content-Type: text/plain; charset="Windows-1252"
>
> Thanks Louis , Mallar and team for the great support over many years.
>
> Even if some of our pipelines have evolved to use other tools as well,  yes my team and I are still using Minc !
>
> Cordially
>
> Christophe
>
> ___________________________________________________________________
> Christophe Grova, PhD
> Professor, Physics Dpt, Concordia University
> Concordia School of Health
>
> Adjunct Prof in Biomedical Engineering, and Neurology and Neurosurgery Dpt, McGill University
> Multimodal Functional Imaging Lab (Multi FunkIm)
> Montreal Neurological Institute - epilepsy group
> Centre de Recherches en Math?matiques
>
> Physics Dpt Concordia University - Loyola Campus - Office SP 265.02
> 7141 Sherbrooke Street West, Montreal, QC  H4B 1R6
>
> Phone: (514) 848-2424 ext.4221
> email : christophe.grova at concordia.ca , christophe.grova at mcgill.ca
> Explore Concordia: http://explore.concordia.ca/christophe-grova
> Physics, Concordia University: https://www.concordia.ca/faculty/christophe-grova.html
> MultiFunkIm Lab: https://www.multifunkim.com<https://www.multifunkim.com/>
> ______________________________________________________________
>
> ________________________________
> From: MINC-users <minc-users-bounces at bic.mni.mcgill.ca> on behalf of Louis Collins, Mr <louis.collins at mcgill.ca>
> Sent: Monday, May 26, 2025 10:19 AM
> 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.
>
> 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
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 27 May 2025 20:56:11 +0900
> From: Khoo Hui Ming <khoo at nsurg.med.osaka-u.ac.jp>
> 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:
> 	<CABDwP5FExwM9Db+d+OA2oQyRNp4=88vs3NuTYzsZZ7Pf8GkQKQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Louis,
>
> Thank you for the support that you and your team have been doing over all
> these years.
>
> Yes, I am still using minc even though I have moved from Montreal to Japan.
> I will continue to use minc if the support can be sustained in the future.
>
> Thank you.
>
> Best regards,
>
> Hui Ming Khoo, MD, PhD
> Assistant Professor,
> Department of Neurosurgery,
> Osaka University,
> Suita, Japan.
>
>
>
> On Mon, 26 May 2025, 23:19 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
>>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 27 May 2025 12:15:57 +0000
> From: John Sled <john.sled at utoronto.ca>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Cc: Brian Nieman <brian.nieman at sickkids.ca>
> Subject: Re: [MINC-users] the future of MINC and MINC support - need 2
> 	min.
> Message-ID:
> 	<YT2PR01MB4416D86129B7C66DD48F43B3E364A at YT2PR01MB4416.CANPRD01.PROD.OUTLOOK.COM>
> 	
> Content-Type: text/plain; charset="utf-8"
>
> Hi Louis,
>
> The Mouse Imaging Centre is very invested in MINC too and we use it for all our imaging modalities ? MRI, CT, ultrasound, optical.   We rarely use dicom data though and I had not been aware of the dicom conversion issue you mentioned.  I think keeping MINC alive is worthwhile.  Tracking vendor DICOM format changes is a Sisyphean task though.  I wonder if the way forward is to convert files to MINC via NIFTI/BIDS or some other intermediary.
>
> cheers,
>
> John
>
>
> --------------------------------------------------------------------------
> John G. Sled, Ph.D.
> Senior Scientist, Hospital for Sick Children
> Canada Research Chair in Biomedical Imaging
> Professor and Vice-Chair, Department of Medical Biophysics,
>    University of Toronto
>
> Hospital for Sick Children                       Phone: 416 813-7654 x309557
> Mouse Imaging Centre                             Fax: 647 837-5832
> 555 University Avenue                            Email: john.sled at utoronto.ca
> Toronto, Ontario
> M5G 1X8 Canada
>
> From: MINC-users <minc-users-bounces at bic.mni.mcgill.ca> on behalf of Khoo Hui Ming <khoo at nsurg.med.osaka-u.ac.jp>
> Date: Tuesday, May 27, 2025 at 7:57?AM
> 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.
> [You don't often get email from khoo at nsurg.med.osaka-u.ac.jp. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
>
> Hi Louis,
>
> Thank you for the support that you and your team have been doing over all
> these years.
>
> Yes, I am still using minc even though I have moved from Montreal to Japan.
> I will continue to use minc if the support can be sustained in the future.
>
> Thank you.
>
> Best regards,
>
> Hui Ming Khoo, MD, PhD
> Assistant Professor,
> Department of Neurosurgery,
> Osaka University,
> Suita, Japan.
>
>
>
> On Mon, 26 May 2025, 23:19 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
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
> ------------------------------
>
> End of MINC-users Digest, Vol 177, Issue 2
> ******************************************

-- 
Daniel Hoops
danielhoops.com