[MINC-development] dcm2mnc issues
Alex Zijdenbos
zijdenbos at gmail.com
Mon Jun 14 11:19:44 EDT 2021
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>
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>
> 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
>>> >> _______________________________________________
>>> >> MINC-development mailing list
>>> >> MINC-development at bic.mni.mcgill.ca
>>> >> <mailto:MINC-development at bic.mni.mcgill.ca>
>>> >>
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>>> >> <
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
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>>> >
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>>> >>
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>>> >> <
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>> <https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$>
>>> >
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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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>> _______________________________________________
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>
>
> --
> Best regards,
>
> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
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