From louis.collins at mcgill.ca Mon May 26 10:19:28 2025 From: louis.collins at mcgill.ca (Louis Collins, Mr) Date: Mon, 26 May 2025 14:19:28 +0000 Subject: [MINC-users] the future of MINC and MINC support - need 2 min. Message-ID: 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 From simone at biospective.com Mon May 26 11:32:16 2025 From: simone at biospective.com (Simone Zehntner) Date: Mon, 26 May 2025 11:32:16 -0400 Subject: [MINC-users] the future of MINC and MINC support - need 2 min. In-Reply-To: References: Message-ID: 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 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 > From zijdenbos at gmail.com Mon May 26 15:20:36 2025 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Mon, 26 May 2025 15:20:36 -0400 Subject: [MINC-users] the future of MINC and MINC support - need 2 min. In-Reply-To: References: Message-ID: 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 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 > > From christophe.grova at mcgill.ca Tue May 27 07:06:50 2025 From: christophe.grova at mcgill.ca (Christophe Grova, M) Date: Tue, 27 May 2025 11:06:50 +0000 Subject: [MINC-users] the future of MINC and MINC support - need 2 min. In-Reply-To: References: Message-ID: 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 ______________________________________________________________ ________________________________ From: MINC-users on behalf of Louis Collins, Mr Sent: Monday, May 26, 2025 10:19 AM To: 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 From khoo at nsurg.med.osaka-u.ac.jp Tue May 27 07:56:11 2025 From: khoo at nsurg.med.osaka-u.ac.jp (Khoo Hui Ming) Date: Tue, 27 May 2025 20:56:11 +0900 Subject: [MINC-users] the future of MINC and MINC support - need 2 min. In-Reply-To: References: Message-ID: 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, 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 > From john.sled at utoronto.ca Tue May 27 08:15:57 2025 From: john.sled at utoronto.ca (John Sled) Date: Tue, 27 May 2025 12:15:57 +0000 Subject: [MINC-users] the future of MINC and MINC support - need 2 min. In-Reply-To: References: Message-ID: 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 on behalf of Khoo Hui Ming Date: Tuesday, May 27, 2025 at 7:57?AM To: MINC users mailing list 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, 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 From mallar.chak at gmail.com Tue May 27 09:09:46 2025 From: mallar.chak at gmail.com (Mallar Chakravarty) Date: Tue, 27 May 2025 09:09:46 -0400 Subject: [MINC-users] the future of MINC and MINC support - need 2 min. In-Reply-To: References: Message-ID: Hello all, Just wanted to chime in. We're using MINC actively over at Douglas. Especially as we tread into new modalities and contrasts on the animal imaging side. Having the flexibility that minc offers has been extremely valuable. mallar On Tue, May 27, 2025 at 8:16?AM John Sled wrote: > 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 on behalf of Khoo > Hui Ming > Date: Tuesday, May 27, 2025 at 7:57?AM > To: MINC users mailing list > 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, > 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 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From daniel.hoops at mail.mcgill.ca Tue May 27 09:43:42 2025 From: daniel.hoops at mail.mcgill.ca (Daniel Hoops) Date: Tue, 27 May 2025 23:43:42 +1000 Subject: [MINC-users] MINC-users Digest, Vol 177, Issue 2 In-Reply-To: References: Message-ID: <37932890-c825-4608-ac25-d517ea970971@mail.mcgill.ca> 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: > Send MINC-users mailing list submissions to > minc-users at bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users > or, via email, send a message with subject or body 'help' to > minc-users-request at bic.mni.mcgill.ca > > You can reach the person managing the list at > minc-users-owner at bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MINC-users digest..." > > > 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 > To: MINC users mailing list > Subject: Re: [MINC-users] the future of MINC and MINC support - need 2 > min. > Message-ID: > > 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 > 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" > To: "minc-users at bic.mni.mcgill.ca" > Subject: Re: [MINC-users] the future of MINC and MINC support - need 2 > min. > Message-ID: > > > 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 > ______________________________________________________________ > > ________________________________ > From: MINC-users on behalf of Louis Collins, Mr > Sent: Monday, May 26, 2025 10:19 AM > To: 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 > To: MINC users mailing list > Subject: Re: [MINC-users] the future of MINC and MINC support - need 2 > min. > Message-ID: > > 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, > 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 > To: MINC users mailing list > Cc: Brian Nieman > Subject: Re: [MINC-users] the future of MINC and MINC support - need 2 > min. > Message-ID: > > > 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 on behalf of Khoo Hui Ming > Date: Tuesday, May 27, 2025 at 7:57?AM > To: MINC users mailing list > 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, > 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 From a.janke at gmail.com Tue May 27 16:18:06 2025 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 28 May 2025 06:18:06 +1000 Subject: [MINC-users] the future of MINC and MINC support - need 2 min. In-Reply-To: References: Message-ID: 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 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 > From mastaneht.83 at gmail.com Thu May 29 04:29:00 2025 From: mastaneht.83 at gmail.com (Mastaneh Torkamani) Date: Thu, 29 May 2025 11:29:00 +0300 Subject: [MINC-users] the future of MINC and MINC support - need 2 min In-Reply-To: References: Message-ID: 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 wrote: > Send MINC-users mailing list submissions to > minc-users at bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users > or, via email, send a message with subject or body 'help' to > minc-users-request at bic.mni.mcgill.ca > > You can reach the person managing the list at > minc-users-owner at bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MINC-users digest..." > > > Today's Topics: > > 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" > To: "minc-users at bic.mni.mcgill.ca" > Subject: [MINC-users] the future of MINC and MINC support - need 2 > min. > Message-ID: > 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 > To: MINC users mailing list > 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 > > > > > ------------------------------ > > 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 1 > ****************************************** > From sean at rogue-research.com Fri May 30 18:09:51 2025 From: sean at rogue-research.com (Sean McBride) Date: Fri, 30 May 2025 18:09:51 -0400 Subject: [MINC-users] the future of MINC and MINC support - need 2 min. In-Reply-To: References: Message-ID: <17381A89-0545-434D-B207-111EC51A51B8@rogue-research.com> 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.