<div dir="ltr">Hi Alfredo,<div><br></div><div>I was told you were given access to MCIN's loris-mri channel. Let me know if you can login successfully.</div><div><br></div><div><br></div><div>Nicolas</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 22, 2020 at 8:45 AM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu">AMORALESPINZON@bwh.harvard.edu</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 style="overflow-wrap: break-word;">
Hi Nicolas,
<div><br>
</div>
<div>Thank you for your answer. I will prepare some screenshots before our meeting. What slack group should I join?</div>
<div><br>
</div>
<div>Best,</div>
<div>Alfredo.<br>
<div><br>
<blockquote type="cite">
<div>On Apr 21, 2020, at 9:48 AM, Nicolas Brossard <<a href="mailto:nicolasbrossard.mni@gmail.com" target="_blank">nicolasbrossard.mni@gmail.com</a>> wrote:</div>
<br>
<div>
<p><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)"> External Email - Use Caution </span></p>
<div><br>
</div>
<div dir="ltr">Hi Alfredo,
<div><br>
</div>
<div>When you say that you can still see those visits, I assume that you are saying that they are still listed on the time point list page for a given candidate even though you were not expecting them to be. Is that correct? And you are also saying
that there is still a clickable 'Yes' in the 'Imaging Scan Done' column for that visit that leads nowhere (i.e broken link), right? Just trying to make sure I understand the observed behaviour.</div>
<div><br>
</div>
<div>I have been very unsuccessful running both Zoom and slack phone call on my computer. My laptop has has some kind of hardware problem that makes it crash very often when I run video intensive softwares like these (it tends to shutdown after 5-10
mins. or so, as I have often experienced during the remote LORIS meetings....) We could talk via slack (no video) if you like. Let me know what you think is best.</div>
<div><br>
</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Nicolas</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Apr 20, 2020 at 3:55 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</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>Hi Nicolas,
<div><br>
</div>
<div>I change the Scan_Done value from ‘Y’ to ’N’ but I still can see these visits and links, which seem to be broken links, in the front-end. Any ideas? We can arrange a Zoom call if this helps us to figure things out.</div>
<div><br>
</div>
<div>Best,</div>
<div>Alfredo.</div>
<div>
<div><br>
<blockquote type="cite">
<div>On Apr 16, 2020, at 9:05 AM, Nicolas Brossard <<a href="mailto:nicolasbrossard.mni@gmail.com" target="_blank">nicolasbrossard.mni@gmail.com</a>> wrote:</div>
<br>
<div>
<p><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)"> External Email - Use Caution </span></p>
<div><br>
</div>
<div dir="ltr">Hi Alfredo,
<div><br>
</div>
<div>If none of the INSERT statements have a session ID of 845, then that session was not related in any way to the uploads you deleted. Consequently, I think that the behaviour of the delete script is totally unrelated to the fact that session 845
has scan_done = 'Y' even though it is not tied to any archive. When you start a visit, you have to specify whether a scan was done or not and the system will not immediately "force" you to upload scans if you indicated that a scan was done. It is thus entirely
possible that:</div>
<div><br>
</div>
<div>1. Session 845 was started and the user who started it indicated that a scan was done.</div>
<div>2. No scans were uploaded afterwards for that session....</div>
<div><br>
</div>
<div>I personally think this behaviour is not desirable and the Scan_done flag should only be set to 'Yes' if the session is tied to an existing archive. If you also agree, you can just identify the sessions that do not fill this requirement and set
their Scan_Done flag to 'No'.</div>
<div><br>
</div>
<div>Hope that help!</div>
<div><br>
</div>
<div><br>
</div>
<div>Best,</div>
<div>Nicolas</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Apr 16, 2020 at 12:04 AM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</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>Hi Nicolas,
<div><br>
</div>
<div>I checked the INSERT statements but no one has a SessionID set to 845.</div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div dir="ltr">
<div>Also, are you sure you did not manually delete records from mri_upload after the delete script was run?</div>
</div>
</blockquote>
<div><br>
</div>
Yes, I’ve only used the script. However, I recall that during the insertion of this study I had issues with the insertion of the images, for instance I had errors in the middle of the pipeline.</div>
<div><br>
</div>
<div>Let me know if a call can be helpful to figure this out faster.</div>
<div><br>
</div>
<div>Best,</div>
<div>Alfredo.<br>
<div><br>
<blockquote type="cite">
<div>On Apr 15, 2020, at 3:42 PM, Nicolas Brossard <<a href="mailto:nicolasbrossard.mni@gmail.com" target="_blank">nicolasbrossard.mni@gmail.com</a>> wrote:</div>
<br>
<div>
<p><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)"> External Email - Use Caution </span></p>
<div><br>
</div>
<div dir="ltr">Hi Alfredo,
<div><br>
</div>
<div>Yep, all clear. Tables mri_upload and tarchive both have a column SessionID. You said you did not find in your backup files an UPDATE statement for session 845. Can you check in your backup files the INSERT statements for tables mri_upload and
tarchive? Do any of these statements have a SessionID set to 845?</div>
<div><br>
</div>
<div>Also, are you sure you did not manually delete records from mri_upload after the delete script was run?</div>
<div><br>
</div>
<div><br>
</div>
<div>Best,</div>
<div>Nicolas</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Apr 15, 2020 at 3:32 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</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>Hi Nicolas,
<div><br>
</div>
<div>Apologies for not being clear in my last email. I meant to say that after removing 3200 upload ids and didn’t find the session 845 in any of the backup SQL generated files. I have multiple back up files as I removed the 3200 ids one by one. Is
it clear now?</div>
<div><br>
</div>
<div>Best,</div>
<div>Alfredo.</div>
<div>
<div><br>
<blockquote type="cite">
<div>On Apr 15, 2020, at 2:17 PM, Nicolas Brossard <<a href="mailto:nicolasbrossard.mni@gmail.com" target="_blank">nicolasbrossard.mni@gmail.com</a>> wrote:</div>
<br>
<div>
<p><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)"> External Email - Use Caution </span></p>
<div><br>
</div>
<div dir="ltr">Hi Alfredo,
<div><br>
</div>
<div>So what you are saying is that the script deleted a record in table mri_upload with uploadid = 3200 but there was no corresponding UPDATE session statement? In your previous email you were referring to a session with ID 845 that had scan_done
set to 'Y' even though there were no archives associated to it. Was the mri_upload with uploadid 3200 tied to session 845? Are you able to see in the backup file all the mri_uploads tied to session 845 that were deleted? </div>
<div><br>
</div>
<div><br>
</div>
<div>Nicolas</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Apr 15, 2020 at 12:51 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</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>Hi Nicolas,
<div><br>
</div>
<div>I checked the records, for the 3200 deleted uploadId, and the sessionID was not in there. Also, the UPDATE statement was issues in the same table. Here is an example of INSERT and UPDATE commands in the SQL file:</div>
<div><br>
</div>
<div>===</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"><font>INSERT INTO `mri_upload` VALUES (9,'lorisadmin\n','2017-11-28 16:30:47',’/ABC/AAB21935_880779_m00.tar.gz','/tmp/ImagingUpload-16-30-jIjf1G',1,0,'AAB21935_880779_m00',8,8,6,</font><font color="#ff1f00">4</font><font>,1,1,'N');</font></span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">UPDATE session s SET Scan_done = 'Y' WHERE s.ID IN (4) AND (SELECT COUNT(*) FROM mri_upload m WHERE m.SessionID=s.ID) > 0; </span></div>
</div>
<div>===</div>
<div><br>
</div>
<div>Maybe the insertion process didn’t finish properly but the state of the database was updated? As you can see this images were uploaded in 2017 using LORIS v17.0.0 or v18.0.0. Let me know if you have more suggestions on what to check and how we
can solve this.</div>
<div><br>
</div>
<div>Best,</div>
<div>Alfredo.</div>
<div>
<div><br>
<blockquote type="cite">
<div>On Apr 13, 2020, at 8:37 PM, Nicolas Brossard <<a href="mailto:nicolasbrossard.mni@gmail.com" target="_blank">nicolasbrossard.mni@gmail.com</a>> wrote:</div>
<br>
<div>
<p><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)"> External Email - Use Caution </span></p>
<div><br>
</div>
<div dir="ltr">Hi Alfredo,
<div><br>
</div>
<div>I am curious to see the actual records that the delete script removed from your mri_upload table. Since the delete script backs up what it deletes, you can have a look inside the backup file it created. By default, this file is named imaging_upload_backup.tar.gz.
Inside, you'll find an SQL file that should contain all the entries in mri_upload that were deleted. Can you check if all of them have a sessionID set to 845 (they should)? Can you also check in the same file the UPDATE statement that was issued on the session
table? We'll start with these checks first.</div>
<div><br>
</div>
<div><br>
</div>
<div>Best,</div>
<div>Nicolas</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Apr 13, 2020 at 8:16 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</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>Dear LorisDev Team,
<div><br>
</div>
<div>I recently removed all the UploadIDs from a study using the script “<font face="Helvetica Neue"><span><a href="http://delete_imaging_upload.pl/" target="_blank">delete_imaging_upload.pl</a></span><span>”</span><span>.
However, in the front-end I can see some </span><span>imaging visits for some candidates of the study. </span></font></div>
<div><font face="Helvetica Neue"><span><br>
</span></font></div>
<div><font face="Helvetica Neue"><span>Here is an example for one visit:</span></font></div>
<div><br>
</div>
<div>Here is the imaging session for one the Candidates with the issue:</div>
<div><font face="Helvetica Neue"><span>===</span></font></div>
<div>
<div><font face="Menlo">select * from session where CandID in (450030) \G;</font></div>
<div><font face="Menlo">*************************** 1. row ***************************</font></div>
<div><font face="Menlo"> <font color="#ff1f00">
ID: 845</font></font></div>
<div><font face="Menlo"> CandID: 450030</font></div>
<div><font face="Menlo"> CenterID: 60</font></div>
<div><font face="Menlo"> VisitNo: 1</font></div>
<div><font face="Menlo"> Visit_label: m00</font></div>
<div><font face="Menlo"> SubprojectID: 2</font></div>
<div><font face="Menlo"> Submitted: N</font></div>
<div><font face="Menlo"> Current_stage: Not Started</font></div>
<div><font face="Menlo"> Date_stage_change: NULL</font></div>
<div><font face="Menlo"> Screening: NULL</font></div>
<div><font face="Menlo"> Date_screening: NULL</font></div>
<div><font face="Menlo"> Visit: NULL</font></div>
<div><font face="Menlo"> Date_visit: NULL</font></div>
<div><font face="Menlo"> Approval: NULL</font></div>
<div><font face="Menlo"> Date_approval: NULL</font></div>
<div><font face="Menlo"> Active: Y</font></div>
<div><font face="Menlo"> Date_active: 2017-11-10</font></div>
<div><font face="Menlo"> RegisteredBy: 5216-ICR_dataman</font></div>
<div><font face="Menlo"> UserID: 5216-ICR_dataman</font></div>
<div><font face="Menlo"> Date_registered: 2017-11-10</font></div>
<div><font face="Menlo"> Testdate: 2017-11-30 11:07:25</font></div>
<div><font face="Menlo"> Hardcopy_request: -</font></div>
<div><font face="Menlo"> BVLQCStatus: NULL</font></div>
<div><font face="Menlo"> BVLQCType: NULL</font></div>
<div><font face="Menlo"> BVLQCExclusion: NULL</font></div>
<div><font face="Menlo"> QCd: NULL</font></div>
<div><font face="Menlo"> <font color="#ff1f00">
Scan_done: Y</font></font></div>
<div><font face="Menlo"> MRIQCStatus:</font></div>
<div><font face="Menlo"> MRIQCPending: N</font></div>
<div><font face="Menlo">MRIQCFirstChangeTime: NULL</font></div>
<div><font face="Menlo"> MRIQCLastChangeTime: NULL</font></div>
<div><font face="Menlo"> MRICaveat: false</font></div>
</div>
<div><font face="Helvetica Neue"><span>===</span></font></div>
<div><font face="Helvetica Neue"><span><br>
</span></font></div>
<div><font face="Helvetica Neue"><span>However, there is no TarchiveID associated with the session id in the mri_upload table</span></font></div>
<div><span><font face="Menlo">===</font></span></div>
<div><span><font face="Menlo">
<div><span>select TarchiveID from mri_upload where SessionID=</span><font color="#ff1f00">845</font><span> \G;</span></div>
<div>Empty set (0.00 sec)</div>
</font></span></div>
<div><span><font face="Menlo">===</font></span></div>
<div><font face="Helvetica Neue"><span><br>
</span></font></div>
<div><font face="Helvetica Neue"><span>Any ideas on how can I fix this.</span></font></div>
<div><font face="Helvetica Neue"><span><br>
</span></font></div>
<div><font face="Helvetica Neue"><span>Thank you in advance for your help.</span></font></div>
<div><font face="Helvetica Neue"><span><br>
</span></font></div>
<div><font face="Helvetica Neue"><span>Regards,</span></font></div>
<div><font face="Helvetica Neue"><span>Alfredo.</span></font></div>
<div><font face="Helvetica Neue"><span><br>
</span></font></div>
<div><font face="Helvetica Neue"><span><br>
</span></font></div>
</div>
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