<div dir="ltr">Hi Cecile, others,<div><br></div><div>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...</div><div><br></div><div>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.</div><div><br></div><div>-- A</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jun 14, 2021 at 10:21 AM Vladimir S. FONOV <<a href="mailto:vladimir.fonov@gmail.com">vladimir.fonov@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">So,<div><br></div><div>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.</div><div><br></div><div>Unless I misunderstand who "we" is in this context. </div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jun 14, 2021 at 9:28 AM Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>Thank you for the suggestion!<br><div><br></div><div>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. </div><div><br></div><div>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 :).</div><div><br></div><div>Thanks again for the suggestion!</div><div><br></div><div>Cécile</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Jun 12, 2021 at 2:05 PM Ben Darwin <<a href="mailto:benjamin.darwin@sickkids.ca" target="_blank">benjamin.darwin@sickkids.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
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.<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Regards,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Ben<br>
</div>
<div id="gmail-m_-2392749426726865899gmail-m_1292857155123272162gmail-m_-4295273245247205851appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-2392749426726865899gmail-m_1292857155123272162gmail-m_-4295273245247205851divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> <a href="mailto:minc-development-bounces@bic.mni.mcgill.ca" target="_blank">minc-development-bounces@bic.mni.mcgill.ca</a> <<a href="mailto:minc-development-bounces@bic.mni.mcgill.ca" target="_blank">minc-development-bounces@bic.mni.mcgill.ca</a>> on behalf of Vladimir S. FONOV <<a href="mailto:vladimir.fonov@gmail.com" target="_blank">vladimir.fonov@gmail.com</a>><br>
<b>Sent:</b> June 11, 2021 3:52 PM<br>
<b>To:</b> MINC development discussion & planning <<a href="mailto:minc-development@bic.mni.mcgill.ca" target="_blank">minc-development@bic.mni.mcgill.ca</a>><br>
<b>Subject:</b> Re: [MINC-development] dcm2mnc issues</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hello Cecile,
<div><br>
</div>
<div>I will talk to my people, ask them how motivated they are to fix this issue. </div>
</div>
<br>
<div>
<div dir="ltr">On Fri, Jun 11, 2021 at 2:58 PM Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hello MINC developers,
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Link to the issues: <a href="https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL0_HLvv4$" target="_blank">https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar</a> </div>
<div><br>
</div>
<div>As Vlad pointed out (thank you for testing Vlad!!(, the issues do not seem to be resolved. See <a href="https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/pull/113__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL_v6TmU6$" target="_blank">https://github.com/BIC-MNI/minc-tools/pull/113</a></div>
<div>If we could have some updates on the plan moving forward, that would be greatly appreciated.<br>
</div>
<div><br>
</div>
<div>Crossing my fingers that those issues could be resolved. </div>
<div>Keep me posted. Thank you! </div>
<div><br>
</div>
<div>Cécile</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, May 19, 2021 at 12:08 AM Vladimir S. FONOV <<a href="mailto:vladimir.fonov@gmail.com" target="_blank">vladimir.fonov@gmail.com</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Unfortunately, proposed changes do not seem to address the problem.
<div>See <a href="https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/pull/113__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL_v6TmU6$" target="_blank">https://github.com/BIC-MNI/minc-tools/pull/113</a></div>
</div>
<br>
<div>
<div dir="ltr">On Fri, May 7, 2021 at 1:35 PM Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi Vlad,<br>
<br>
Definitely, I will copy sample datasets and let you know where they are once copied. Thank you!!<br>
<br>
Cécile<br>
<br>
> On May 7, 2021, at 10:36 AM, Vladimir S. Fonov <<a href="mailto:vladimir.fonov@gmail.com" target="_blank">vladimir.fonov@gmail.com</a>> wrote:<br>
> <br>
> Hello,<br>
> <br>
> <br>
> so the proposed change to the minc-tools is on github ( <a href="https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/pull/113__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL_v6TmU6$" rel="noreferrer" target="_blank">
https://github.com/BIC-MNI/minc-tools/pull/113</a> ), but there is no DICOM files to actually test that it works.<br>
> <br>
> So, as an interested party, perhaps Cecile Madjar can supply a set of DICOMs that can be used for testing?<br>
> <br>
> <br>
> On 2021-04-30 10:02 a.m., Cecile Madjar wrote:<br>
>> Hi JP,<br>
>> This is great news! Thank you. Let me know once it is part of the MINC tools.<br>
>> Is there a way to obtain the dcm2mnc binaries for Ubuntu and CentOS at the same time by any chance?<br>
>> Thank you again,<br>
>> Cécile<br>
>> On Thu, Apr 29, 2021 at 1:05 PM Jean-Philippe Coutu <<a href="mailto:jp@biospective.com" target="_blank">jp@biospective.com</a> <mailto:<a href="mailto:jp@biospective.com" target="_blank">jp@biospective.com</a>>> wrote:<br>
>> Hi Cecile,<br>
>> We have been modifying dcm2mnc actively internally over the past<br>
>> four years without having the bandwidth to generate pull requests to<br>
>> the minctools github repository. I am preparing a (sizeable) pull<br>
>> request to the minctools github repository that includes all of our<br>
>> changes, which I believe from my experience is likely to fix at<br>
>> least two of the three issues you have opened.<br>
>> Best,<br>
>> JP<br>
>> From: *Cecile Madjar* <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a><br>
>> <mailto:<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>>><br>
>> Date: Fri, Apr 23, 2021 at 5:22 PM<br>
>> Subject: [MINC-development] dcm2mnc issues<br>
>> To: MINC development discussion & planning<br>
>> <<a href="mailto:minc-development@bic.mni.mcgill.ca" target="_blank">minc-development@bic.mni.mcgill.ca</a><br>
>> <mailto:<a href="mailto:minc-development@bic.mni.mcgill.ca" target="_blank">minc-development@bic.mni.mcgill.ca</a>>>,<br>
>> <<a href="mailto:minc-users@bic.mni.mcgill.ca" target="_blank">minc-users@bic.mni.mcgill.ca</a> <mailto:<a href="mailto:minc-users@bic.mni.mcgill.ca" target="_blank">minc-users@bic.mni.mcgill.ca</a>>><br>
>> Hello,<br>
>> A while back, we logged several critical dcm2mnc issues on<br>
>> GitHub. We are still experiencing those issues in several of our<br>
>> LORIS projects. I wanted to follow up with the MINC community<br>
>> regarding those issues to see if dcm2mnc is still supported and<br>
>> if there will be any developments regarding those issues.<br>
>> Here is the list of logged issues:<br>
>> <a href="https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL0_HLvv4$" rel="noreferrer" target="_blank">
https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar</a><br>
>> <<a href="https://urldefense.com/v3/__https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL0_HLvv4$" rel="noreferrer" target="_blank">https://github.com/BIC-MNI/minc-tools/issues/created_by/cmadjar</a>><br>
>> As the imaging world progresses, we are encountering those<br>
>> problematic issues in more of our LORIS projects and we need to<br>
>> provide our users solutions regarding these issues. If there is<br>
>> no possibility to fix dcm2mnc, then we may have to consider<br>
>> moving away from MINC, which we would prefer avoiding for<br>
>> obvious reasons.<br>
>> Please, let us know your thoughts on this. Help regarding these<br>
>> issues would be greatly appreciated.<br>
>> Best regards,<br>
>> Cécile<br>
>> _______________________________________________<br>
>> MINC-development mailing list<br>
>> <a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
>> <mailto:<a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a>><br>
>> <a href="https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
>> <<a href="https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$" rel="noreferrer" target="_blank">https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a>><br>
>> _______________________________________________<br>
>> MINC-development mailing list<br>
>> <a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
>> <mailto:<a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a>><br>
>> <a href="https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
>> <<a href="https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$" rel="noreferrer" target="_blank">https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a>><br>
>> _______________________________________________<br>
>> MINC-development mailing list<br>
>> <a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
>> <a href="https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
> <br>
> _______________________________________________<br>
> MINC-development mailing list<br>
> <a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
> <a href="https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
<br>
<br>
_______________________________________________<br>
MINC-development mailing list<br>
<a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
<a href="https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$" rel="noreferrer" target="_blank">https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">Best regards,<br>
<br>
Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com</div>
_______________________________________________<br>
MINC-development mailing list<br>
<a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
<a href="https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$" rel="noreferrer" target="_blank">https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
</blockquote>
</div>
_______________________________________________<br>
MINC-development mailing list<br>
<a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
<a href="https://urldefense.com/v3/__https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development__;!!D0zGoin7BXfl!qqNkMRvBKmkB9bZlPSjbe6qInGLWTyIbSl_EvjKGVEV2CXRU4iSVVpVArtIBtBANL5rYh5CT$" rel="noreferrer" target="_blank">https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">Best regards,<br>
<br>
Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com</div>
</div>
<br>
<hr>
<font face="Arial" color="Gray" size="1"><br>
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than
the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.<br>
</font>
</div>
_______________________________________________<br>
MINC-development mailing list<br>
<a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
<a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development" rel="noreferrer" target="_blank">https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
</blockquote></div>
_______________________________________________<br>
MINC-development mailing list<br>
<a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
<a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development" rel="noreferrer" target="_blank">https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr">Best regards,<br><br> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com</div></div>
_______________________________________________<br>
MINC-development mailing list<br>
<a href="mailto:MINC-development@bic.mni.mcgill.ca" target="_blank">MINC-development@bic.mni.mcgill.ca</a><br>
<a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development" rel="noreferrer" target="_blank">https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development</a><br>
</blockquote></div>