From vladimir.fonov at gmail.com  Fri May  7 10:36:37 2021
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Fri, 7 May 2021 10:36:37 -0400
Subject: [MINC-development] dcm2mnc issues
In-Reply-To: <CAMkiY3dnynsYOZ++gAGQe820Kc2oueWdf55pqXEoc9tcOwnL6w@mail.gmail.com>
References: <CAMkiY3eizfR7OAab_50-sbfMUQYzT_Gpfr+51WR147EXNy1h5g@mail.gmail.com>
 <CABApf9HErmshPtOe2Kx2xqxjLpwuvA_C2OU1=9_wtMG6fpE0ww@mail.gmail.com>
 <CANHs=MdJr1j0WMLUF1ragyaNwJuU_RvaQ75=-hdFMghVGKB4Dw@mail.gmail.com>
 <CAMkiY3dnynsYOZ++gAGQe820Kc2oueWdf55pqXEoc9tcOwnL6w@mail.gmail.com>
Message-ID: <2fa2afbd-9e3e-0e3d-fd70-0be1a85e6790@gmail.com>

Hello,


so the proposed change to the minc-tools is on github ( 
https://github.com/BIC-MNI/minc-tools/pull/113 ), 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,
> 
> C?cile
> 
> 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://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar>
> 
>         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,
> 
>         C?cile
> 
> 
>         _______________________________________________
>         MINC-development mailing list
>         MINC-development at bic.mni.mcgill.ca
>         <mailto:MINC-development at bic.mni.mcgill.ca>
>         https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>         <https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development>
> 
>     _______________________________________________
>     MINC-development mailing list
>     MINC-development at bic.mni.mcgill.ca
>     <mailto:MINC-development at bic.mni.mcgill.ca>
>     https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>     <https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development>
> 
> 
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> 


From cecile.madjar at mcin.ca  Fri May  7 13:34:48 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Fri, 7 May 2021 13:34:48 -0400
Subject: [MINC-development] dcm2mnc issues
In-Reply-To: <2fa2afbd-9e3e-0e3d-fd70-0be1a85e6790@gmail.com>
References: <CAMkiY3eizfR7OAab_50-sbfMUQYzT_Gpfr+51WR147EXNy1h5g@mail.gmail.com>
 <CABApf9HErmshPtOe2Kx2xqxjLpwuvA_C2OU1=9_wtMG6fpE0ww@mail.gmail.com>
 <CANHs=MdJr1j0WMLUF1ragyaNwJuU_RvaQ75=-hdFMghVGKB4Dw@mail.gmail.com>
 <CAMkiY3dnynsYOZ++gAGQe820Kc2oueWdf55pqXEoc9tcOwnL6w@mail.gmail.com>
 <2fa2afbd-9e3e-0e3d-fd70-0be1a85e6790@gmail.com>
Message-ID: <D34C9A11-84FC-4B34-913B-C66ECB2C785D@gmail.com>

Hi Vlad,

Definitely, I will copy sample datasets and let you know where they are once copied. Thank you!!

C?cile

> 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 ), 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,
>> C?cile
>> 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://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar>
>>        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,
>>        C?cile
>>        _______________________________________________
>>        MINC-development mailing list
>>        MINC-development at bic.mni.mcgill.ca
>>        <mailto:MINC-development at bic.mni.mcgill.ca>
>>        https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>        <https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development>
>>    _______________________________________________
>>    MINC-development mailing list
>>    MINC-development at bic.mni.mcgill.ca
>>    <mailto:MINC-development at bic.mni.mcgill.ca>
>>    https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>    <https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development>
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> 
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development



From vladimir.fonov at gmail.com  Wed May 19 00:07:53 2021
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 19 May 2021 00:07:53 -0400
Subject: [MINC-development] dcm2mnc issues
In-Reply-To: <D34C9A11-84FC-4B34-913B-C66ECB2C785D@gmail.com>
References: <CAMkiY3eizfR7OAab_50-sbfMUQYzT_Gpfr+51WR147EXNy1h5g@mail.gmail.com>
 <CABApf9HErmshPtOe2Kx2xqxjLpwuvA_C2OU1=9_wtMG6fpE0ww@mail.gmail.com>
 <CANHs=MdJr1j0WMLUF1ragyaNwJuU_RvaQ75=-hdFMghVGKB4Dw@mail.gmail.com>
 <CAMkiY3dnynsYOZ++gAGQe820Kc2oueWdf55pqXEoc9tcOwnL6w@mail.gmail.com>
 <2fa2afbd-9e3e-0e3d-fd70-0be1a85e6790@gmail.com>
 <D34C9A11-84FC-4B34-913B-C66ECB2C785D@gmail.com>
Message-ID: <CAMCwi7PvQNnQFEeQr_cOLosYRbBDc_O76YjGC+LWK_ny9tZrmQ@mail.gmail.com>

Unfortunately, proposed changes do not seem to address the problem.
See https://github.com/BIC-MNI/minc-tools/pull/113

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!!
>
> C?cile
>
> > 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 ), 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,
> >> C?cile
> >> 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://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar
> >
> >>        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,
> >>        C?cile
> >>        _______________________________________________
> >>        MINC-development mailing list
> >>        MINC-development at bic.mni.mcgill.ca
> >>        <mailto:MINC-development at bic.mni.mcgill.ca>
> >>
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> >>        <
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development>
> >>    _______________________________________________
> >>    MINC-development mailing list
> >>    MINC-development at bic.mni.mcgill.ca
> >>    <mailto:MINC-development at bic.mni.mcgill.ca>
> >>    https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> >>    <https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> >
> >> _______________________________________________
> >> MINC-development mailing list
> >> MINC-development at bic.mni.mcgill.ca
> >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> >
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>


-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
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