[MINC-development] dcm2mnc issues

Sat Jun 12 14:04:35 EDT 2021

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