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Hi Ling Ma,
<div class=""><br class="">
</div>
<div class="">You are right, I missed this part in the environment file:</div>
<div class=""><br class="">
</div>
<div class=""><span style="caret-color: rgb(36, 41, 46); color: rgb(36, 41, 46); font-family: SFMono-Regular, Consolas, "Liberation Mono", Menlo, monospace; white-space: pre;" class="">/data/%PROJECT%/bin/mri/dicom-archive</span></div>
<div class=""><font color="#24292e" face="SFMono-Regular, Consolas, Liberation Mono, Menlo, monospace" class=""><span style="caret-color: rgb(36, 41, 46); white-space: pre;" class=""><br class="">
</span></font></div>
<div class=""><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">I have another error now but I guess I need to install Moose module.</span></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class="">
</span></font></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class="">Thank you.</span></font></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class="">
</span></font></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class="">Regards,</span></font></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class="">Alfredo.<br class="">
</span></font>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Mar 30, 2020, at 10:28 PM, Ling Ma <<a href="mailto:lingyun.ma@mcin.ca" class="">lingyun.ma@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 source that environment file? Or you can logout then login to try to activate that file.</div>
<div class=""><br class="">
</div>
<div class="">What you need is: <span style="color:rgb(36,41,46);font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre" class="">PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:/data/%PROJECT%/bin/mri/dicom-archive:$PERL5LIB.</span></div>
<div class="">So I suppose that my suggested method should work for you, if not, try to check PERL5LIB with "echo $PERL5LIB"</div>
<div class=""><br class="">
</div>
<div class="">Good luck.</div>
<div class=""><br class="">
</div>
<div class="">Ling Ma</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Mar 30, 2020 at 10:18 PM 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="">Hi Ling Ma,
<div class=""><br class="">
</div>
<div class="">Thank you for the prompt response.</div>
<div class=""><br class="">
</div>
<div class="">I already had the statement because I am upgrading from v18.0.0. However I double checked and the .bashrc file has the statement. </div>
<div class=""><br class="">
</div>
<div class="">Any other ideas of where to look for?</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Alfredo.<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Mar 30, 2020, at 9:49 PM, Ling Ma <<a href="mailto:lingyun.ma@mcin.ca" target="_blank" class="">lingyun.ma@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="">I believe you need to read the <a href="https://github.com/aces/Loris-MRI/blob/21.0-dev/README.md#5-configure-paths-and-environment" target="_blank" class="">https://github.com/aces/Loris-MRI/blob/21.0-dev/README.md#5-configure-paths-and-environment</a>,
which says:</div>
<div class=""></div>
<div class=""><span style="color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji";font-size:16px" class=""><br class="">
</span></div>
<div class=""><span style="color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji";font-size:16px" class="">"Ensure that /home/lorisadmin/.bashrc includes the statement:</span><br class="">
</div>
<div class="">
<p style="box-sizing:border-box;margin-top:0px;margin-bottom:16px;color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji";font-size:16px" class="">
<code style="box-sizing:border-box;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:13.6px;padding:0.2em 0.4em;margin:0px;background-color:rgba(27,31,35,0.05);border-radius:3px" class="">source /data/$projectname/bin/mri/environment</code></p>
<p style="box-sizing:border-box;margin-top:0px;margin-bottom:16px;color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji";font-size:16px" class="">
Then source the .bashrc file."</p>
<p style="box-sizing:border-box;margin-top:0px;margin-bottom:16px;color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji"" class="">
Regards,<br class="">
</p>
<p style="box-sizing:border-box;margin-top:0px;margin-bottom:16px;color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji"" class="">
Ling Ma</p>
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Mar 30, 2020 at 8:08 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 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="font-family:Menlo;font-size:11px" class=""><a href="http://cleanup_paths_of_violation_tables.pl/" target="_blank" class="">cleanup_paths_of_violation_tables.pl</a></span>”
before running the deletion script but I get the following error:</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures;color:rgb(86,32,244)" class=""><b class="">bin/mri/tools</b></span><span style="font-variant-ligatures:no-common-ligatures" class="">$ perl
<a href="http://cleanup_paths_of_violation_tables.pl/" target="_blank" class="">cleanup_paths_of_violation_tables.pl</a> </span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" 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" 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" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">Compilation failed in require at
<a href="http://cleanup_paths_of_violation_tables.pl/" target="_blank" class="">cleanup_paths_of_violation_tables.pl</a> line 9.</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">BEGIN failed--compilation aborted at
<a href="http://cleanup_paths_of_violation_tables.pl/" target="_blank" class="">cleanup_paths_of_violation_tables.pl</a> line 9.</span></div>
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
<div class="">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" target="_blank" class="">https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/AppendixA-Troubleshooting_guideline.md</a>)</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 9, 2020, at 11:17 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="">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" 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 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 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 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>
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