[MINC-development] dcm2mnc issues
Louis Collins, Dr.
louis.collins at mcgill.ca
Mon Jun 14 15:13:20 EDT 2021
Hi all,
Just a quick note to remind everyone on the list that minc is an open source, community supported, software project. minc is a great file format and API that enables a huge amount of research (and avoids many of the issues related to other file formats like nifti).
While there have been some grants in the past that included specific aims with $$ to support minc, to my knowledge, for at least the past 4-5 years there is no one paid to maintain, upgrade or fix minc. There is no one specifically responsible for minc.
/rant on/
While reaching out to the community is a good thing, and often results in a solution, one can not expect a community of volunteers to drop what they are doing to work (unpaid!) on some minc software issue.
I have supported minc by paying Vlad’s salary out of my grants because I think minc is worthwhile. Mallar has been supporting minc in a similar fashion with Gabriel. It is important to note that neither Mallar or I have grant money specifically to support minc. There has been support in the past from other research groups and some companies that use minc in that they too have made their developers available to work on minc.
I will continue to support minc because I find it useful for projects in my lab. Unfortunately, after 10 or so years paying to help everyone with minc, I can no longer afford to have Vlad spend more than half his time supporting minc and answering questions in minc-users and minc-development. My group will continue focus on minc issues that affect us directly. If this benefits others, then great.
Anyone using minc benefits substantially from the minc community. I would think that anyone using it for big projects that are supported by reasonably big money should discuss with their PIs to decide if they want to support the minc libraries that are at the basis of tools that they benefit from. This support means $$.
/rant off/
I will communicate with the BIC profs to see if there is interest in making the required investments to support minc maintenance and development.
-Louis
> On Jun 14, 2021, at 12:38 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
> Hello Alex and Vlad,
>
> It is wonderful news that Jean-Philippe Coutu brought back your efforts to bring dcm2mnc in line with dcm2niix! I totally understand the complexity of DICOMs, and the ever changing field. Unfortunately, it did not resolve our conversion issues as Vlad pointed out in the PR. Vlad has access to the DICOM files. I am unsure though if we could share those files with Biospective. Samir, would you know?
>
> The real issue is not that there are bugs in the converter. It is totally understandable. The problem is that we have been reaching out to the MINC community (via clear GitHub issues and multiple emails to the mailing lists) for almost 3 years now regarding those specific conversion issues. We have multiple big studies that are using LORIS and that cannot convert their DICOM into MINC images. It is getting quite difficult to justify the issues to them as time passes. We definitely want to keep working with MINC as it has so many benefits but we appear to be having difficulties reaching the MINC community.
>
> We are looking forward to having a solution that solves those dcm2mnc issues.
> Let us know,
>
> Cécile
>
> On Mon, Jun 14, 2021 at 11:20 AM Alex Zijdenbos <zijdenbos at gmail.com <mailto:zijdenbos at gmail.com>> wrote:
> Hi Cecile, others,
>
> We (at Biospective) would also be happy to look at this, but we would need access to the offending DICOM data - if those can be shared, of course...
>
> I should also note that we now and again also run into DICOM data that is simply bad. For sure dcm2mnc is behind dcm2niix and could/should be made more robust (the pull request that Jean-Philippe Coutu posted is a result of our efforts to bring dcm2mnc in line with dcm2niix); but DICOM is such [a mess?] that it likely impossible to develop a converter that will always be able to handle anything that clinical or other acquisition sites produce.
>
> -- A
>
> On Mon, Jun 14, 2021 at 10:21 AM Vladimir S. FONOV <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.com>> wrote:
> So,
>
> Unless I fix the dcm2mnc to support this flavor of DICOMS, MCIN will move away from using MINC. That is going to be an interesting turn of events.
>
> Unless I misunderstand who "we" is in this context.
>
>
> On Mon, Jun 14, 2021 at 9:28 AM Cecile Madjar <cecile.madjar at mcin.ca <mailto:cecile.madjar at mcin.ca>> wrote:
> Hello,
>
> Thank you for the suggestion!
>
> Unfortunately, if we convert DICOM to NIfTI and then convert them to MINC, we lose all the precious header information which we need in our case to automatically identify protocols, database the files and other manipulations. Therefore this is not a viable solution for us unfortunately in our current context.
>
> The best would be to have a working dcm2mnc but if this is something that the MINC community cannot provide, I guess we'll have to move away from MINC altogether, which we would prefer avoiding since MINC is such a great format :).
>
> Thanks again for the suggestion!
>
> Cécile
>
> On Sat, Jun 12, 2021 at 2:05 PM Ben Darwin <benjamin.darwin at sickkids.ca <mailto:benjamin.darwin at sickkids.ca>> wrote:
> A colleague of mine uses dcm2niix (not dcm2nii) followed by nii2mnc and found this combination works well at least for our scans. The DICOM reading part is likely better maintained. Maybe you've tried something similar already, though.
>
> Regards,
>
> Ben
> From: minc-development-bounces at bic.mni.mcgill.ca <mailto:minc-development-bounces at bic.mni.mcgill.ca> <minc-development-bounces at bic.mni.mcgill.ca <mailto:minc-development-bounces at bic.mni.mcgill.ca>> on behalf of Vladimir S. FONOV <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.com>>
> Sent: June 11, 2021 3:52 PM
> To: MINC development discussion & planning <minc-development at bic.mni.mcgill.ca <mailto:minc-development at bic.mni.mcgill.ca>>
> Subject: Re: [MINC-development] dcm2mnc issues
>
> Hello Cecile,
>
> I will talk to my people, ask them how motivated they are to fix this issue.
>
> On Fri, Jun 11, 2021 at 2:58 PM Cecile Madjar <cecile.madjar at mcin.ca <mailto:cecile.madjar at mcin.ca>> wrote:
> Hello MINC developers,
>
> I just wanted to follow up on this issue. Is there a plan to fix the issues I reported with dcm2mnc in the near future?
>
> Link to the issues: https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar <https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL0_HLvv4$>
>
> As Vlad pointed out (thank you for testing Vlad!!(, the issues do not seem to be resolved. See https://github.com/BIC-MNI/minc-tools/pull/113 <https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/pull/113__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL_v6TmU6$>
> If we could have some updates on the plan moving forward, that would be greatly appreciated.
>
> Crossing my fingers that those issues could be resolved.
> Keep me posted. Thank you!
>
> Cécile
>
> On Wed, May 19, 2021 at 12:08 AM Vladimir S. FONOV <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.com>> wrote:
> Unfortunately, proposed changes do not seem to address the problem.
> See https://github.com/BIC-MNI/minc-tools/pull/113 <https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/pull/113__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL_v6TmU6$>
> On Fri, May 7, 2021 at 1:35 PM Cecile Madjar <cecile.madjar at mcin.ca <mailto:cecile.madjar at mcin.ca>> wrote:
> Hi Vlad,
>
> Definitely, I will copy sample datasets and let you know where they are once copied. Thank you!!
>
> Cécile
>
> > On May 7, 2021, at 10:36 AM, Vladimir S. Fonov <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.com>> wrote:
> >
> > Hello,
> >
> >
> > so the proposed change to the minc-tools is on github ( https://github.com/BIC-MNI/minc-tools/pull/113 <https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/pull/113__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL_v6TmU6$> ), but there is no DICOM files to actually test that it works.
> >
> > So, as an interested party, perhaps Cecile Madjar can supply a set of DICOMs that can be used for testing?
> >
> >
> > On 2021-04-30 10:02 a.m., Cecile Madjar wrote:
> >> Hi JP,
> >> This is great news! Thank you. Let me know once it is part of the MINC tools.
> >> Is there a way to obtain the dcm2mnc binaries for Ubuntu and CentOS at the same time by any chance?
> >> Thank you again,
> >> Cécile
> >> On Thu, Apr 29, 2021 at 1:05 PM Jean-Philippe Coutu <jp at biospective.com <mailto:jp at biospective.com> <mailto:jp at biospective.com <mailto:jp at biospective.com>>> wrote:
> >> Hi Cecile,
> >> We have been modifying dcm2mnc actively internally over the past
> >> four years without having the bandwidth to generate pull requests to
> >> the minctools github repository. I am preparing a (sizeable) pull
> >> request to the minctools github repository that includes all of our
> >> changes, which I believe from my experience is likely to fix at
> >> least two of the three issues you have opened.
> >> Best,
> >> JP
> >> From: *Cecile Madjar* <cecile.madjar at mcin.ca <mailto:cecile.madjar at mcin.ca>
> >> <mailto:cecile.madjar at mcin.ca <mailto:cecile.madjar at mcin.ca>>>
> >> Date: Fri, Apr 23, 2021 at 5:22 PM
> >> Subject: [MINC-development] dcm2mnc issues
> >> To: MINC development discussion & planning
> >> <minc-development at bic.mni.mcgill.ca <mailto:minc-development at bic.mni.mcgill.ca>
> >> <mailto:minc-development at bic.mni.mcgill.ca <mailto:minc-development at bic.mni.mcgill.ca>>>,
> >> <minc-users at bic.mni.mcgill.ca <mailto:minc-users at bic.mni.mcgill.ca> <mailto:minc-users at bic.mni.mcgill.ca <mailto:minc-users at bic.mni.mcgill.ca>>>
> >> Hello,
> >> A while back, we logged several critical dcm2mnc issues on
> >> GitHub. We are still experiencing those issues in several of our
> >> LORIS projects. I wanted to follow up with the MINC community
> >> regarding those issues to see if dcm2mnc is still supported and
> >> if there will be any developments regarding those issues.
> >> Here is the list of logged issues:
> >> https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar <https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL0_HLvv4$>
> >> <https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar <https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL0_HLvv4$>>
> >> As the imaging world progresses, we are encountering those
> >> problematic issues in more of our LORIS projects and we need to
> >> provide our users solutions regarding these issues. If there is
> >> no possibility to fix dcm2mnc, then we may have to consider
> >> moving away from MINC, which we would prefer avoiding for
> >> obvious reasons.
> >> Please, let us know your thoughts on this. Help regarding these
> >> issues would be greatly appreciated.
> >> Best regards,
> >> Cécile
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>
> --
> Best regards,
>
> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
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>
> --
> Best regards,
>
> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
>
>
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>
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