<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Cécile and LorisDev team,
<div class=""><br class="">
</div>
<div class="">Indeed, there are some breaking changes so I decided to upgrade to LORIS-MRI v21.0.0. After upgrading I am running the suggested script “ <span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px;" class="">cleanup_paths_of_violation_tables.pl</span>”
before running the deletion script but I get the following error:</div>
<div class="">
<div><br class="">
</div>
<div>===</div>
<div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures; color: #5620f4" class=""><b class="">bin/mri/tools</b></span><span style="font-variant-ligatures: no-common-ligatures" class="">$ perl cleanup_paths_of_violation_tables.pl </span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Can't locate DICOM/DICOM.pm in @INC (you may need to install the DICOM::DICOM module) (@INC contains: /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB
/opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47.</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">BEGIN failed--compilation aborted at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47.</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Compilation failed in require at cleanup_paths_of_violation_tables.pl line 9.</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">BEGIN failed--compilation aborted at cleanup_paths_of_violation_tables.pl line 9.</span></div>
</div>
<div>===</div>
<div><br class="">
</div>
<div>Any idea how to solve it? I couldn’t find it in the troubleshooting guideline (<a href="https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/AppendixA-Troubleshooting_guideline.md" class="">https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/AppendixA-Troubleshooting_guideline.md</a>)</div>
<div><br class="">
</div>
<div>Regards,</div>
<div>Alfredo.</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Mar 9, 2020, at 11:17 AM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<p class=""><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;" class=""> External Email - Use Caution </span></p>
<div class=""><br class="webkit-block-placeholder">
</div>
<div dir="ltr" class="">Hi Alfredo,
<div class=""><br class="">
</div>
<div class="">Have you tested your MRI code since you did the upgrade on the LORIS? There might be some SQL changes impacting the LORIS-MRI side as well (conversion of the ranges in mri_protocol and mri_protocol_checks to MIN and MAX columns for example). </div>
<div class=""><br class="">
</div>
<div class="">If all works well, you can try downloading and testing the<span style="color:rgb(80,0,80)" class=""> </span><a href="http://delete_imaging_upload.pl/" target="_blank" class="">delete_imaging_upload.pl</a> and it may work as is. </div>
<div class=""><br class="">
</div>
<div class="">Let me know how this goes!</div>
<div class=""><br class="">
</div>
<div class="">Cécile</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Mar 9, 2020 at 9:12 AM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;" class="">
<div class="">Dear Loris DevTeam,</div>
<div class=""><br class="">
</div>
<div class="">I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I am currently running v18.0.0. </div>
<div class=""><br class="">
</div>
<div class="">Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, would it be possible to “import” and use
the script <a href="http://delete_imaging_upload.pl/" target="_blank" class="">delete_imaging_upload.pl</a> without upgrading LORIS-MRI?</div>
<div class=""><br class="">
</div>
<div class="">Let me know if this is possible. I would prefer to keep the library as it is cause it’s working perfect for us right now.</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Alfredo.</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Mar 2, 2020, at 12:02 PM, Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@BWH.HARVARD.EDU" target="_blank" class="">AMORALESPINZON@BWH.HARVARD.EDU</a>> wrote:</div>
<br class="">
<div class="">
<div style="overflow-wrap: break-word;" class="">Hi Cécile,
<div class=""><br class="">
</div>
<div class="">I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, <span class="">I am currently running v18.0.0</span>. </div>
<div class=""><br class="">
</div>
<div class=""><span class="">Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, w</span>ould it be possible
to “import” and use the script <a href="http://delete_imaging_upload.pl/" target="_blank" class="">delete_imaging_upload.pl</a> without upgrading LORIS-MRI?</div>
<div class=""><br class="">
</div>
<div class="">Let me know if this is possible. I would prefer to keep the library as it is cause it’s working perfect for us right now.</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Alfredo.</div>
<div class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 4, 2020, at 11:26 AM, Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@BWH.HARVARD.EDU" target="_blank" class="">AMORALESPINZON@BWH.HARVARD.EDU</a>> wrote:</div>
<br class="">
<div class="">
<div style="overflow-wrap: break-word;" class="">Hi Cécile,
<div class=""><br class="">
</div>
<div class="">Thank you for your answer. I will use it once some uploading processes are finished so that I can upgrade LORIS to the its last version where the script is available. I will tell you how it goes.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo.<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 4, 2020, at 9:46 AM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
<br class="">
<div class="">
<p class=""><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)" class=""> External Email - Use Caution </span></p>
<div class=""><br class="">
</div>
<div dir="ltr" class="">Hi Alfredo,
<div class=""><br class="">
</div>
<div class="">Indeed, the <a href="http://delete_imaging_upload.pl/" target="_blank" class="">
delete_imaging_upload.pl</a> script was designed to properly remove imaging dataset without touching the other tables in the database. By defaults, the script will create a backup of the removed dataset (files + MySQL entries) which is always nice to have in
case the delete script was run on a wrong dataset.</div>
<div class=""><br class="">
</div>
<div class="">Run "<a href="http://delete_imaging_upload.pl/" target="_blank" class="">delete_imaging_upload.pl</a> -h " to see the list of options that can be used. </div>
<div class=""><br class="">
</div>
<div class="">Let me know if you have any questions.</div>
<div class=""><br class="">
</div>
<div class="">Cécile</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Feb 3, 2020 at 6:37 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br class="">
</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" class="">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt" class="">
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif" class="">
Hi Cecile,</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif" class="">
<br class="">
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif" class="">
In IPMSA we need to re-upload a whole study in terms of MRI images. Given that I already created all the centers, users in centers, candidates, and visits (clinical and mri), would it be possible to only remove the MRI images previously uploaded? Looking at
the script <a href="https://github.com/aces/Loris-MRI/blob/9fe2972c15e4ddb5da0914d751f9bdb74bf2d7f8/tools/delete_imaging_upload.pl" title="https://github.com/aces/Loris-MRI/blob/9fe2972c15e4ddb5da0914d751f9bdb74bf2d7f8/tools/delete_imaging_upload.pl" style="margin:0px" target="_blank" class="">delete_imaging_upload.pl</a> it
seems to be possible (I can get all the Tarchive IDs assoicated) but I want to confirm before I move forward. Please let me know if this is possible.</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif" class="">
<br class="">
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif" class="">
Thank you for all your help.</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif" class="">
<br class="">
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif" class="">
Regards,</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif" class="">
Alfredo.</div>
</div>
<div id="gmail-m_-5224080615048525280gmail-m_557516744926230718Signature" class="">
<div class=""><br class="">
</div>
</div>
<div class=""><br class="">
</div>
<p class="">The information in this e-mail is intended only for the person to whom it is<br class="">
addressed. If you believe this e-mail was sent to you in error and the e-mail<br class="">
contains patient information, please contact the Partners Compliance HelpLine at<br class="">
<a href="http://www.partners.org/complianceline" target="_blank" class="">http://www.partners.org/complianceline</a> . If the e-mail was sent to you in error<br class="">
but does not contain patient information, please contact the sender and properly<br class="">
dispose of the e-mail.</p>
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>