[MINC-development] dcm2mnc issues
Cecile Madjar
cecile.madjar at mcin.ca
Mon Jun 14 12:38:45 EDT 2021
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> 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> 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
>>>> >> _______________________________________________
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>>>> >>
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>>>> >> <
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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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