[MINC-development] dcm2mnc issues
Vladimir S. FONOV
vladimir.fonov at gmail.com
Mon Jun 14 10:21:24 EDT 2021
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> 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>
> 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 <
>> minc-development-bounces at bic.mni.mcgill.ca> on behalf of Vladimir S.
>> FONOV <vladimir.fonov at gmail.com>
>> *Sent:* June 11, 2021 3:52 PM
>> *To:* MINC development discussion & planning <
>> 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>
>> 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> 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$>
>>
>> On Fri, May 7, 2021 at 1:35 PM Cecile Madjar <cecile.madjar at mcin.ca>
>> wrote:
>>
>> Hi Vlad,
>>
>> Definitely, I will copy sample datasets and let you know where they are
>> once copied. Thank you!!
>>
>> Cécile
>>
>> > On May 7, 2021, at 10:36 AM, Vladimir S. Fonov <
>> vladimir.fonov at gmail.com> wrote:
>> >
>> > Hello,
>> >
>> >
>> > so the proposed change to the minc-tools is on github (
>> https://github.com/BIC-MNI/minc-tools/pull/113
>> <https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/pull/113__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL_v6TmU6$>
>> ), 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>> 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>>
>> >> 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>>,
>> >> <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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>> >
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>> >
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>> >
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>>
>> --
>> Best regards,
>>
>> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
>> _______________________________________________
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>>
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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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