<div dir="ltr"><div>Hi,</div><div><br></div><div>that's the Study Instance UID, not the StudyID. So the StudyID i am looking for is not stored in the database?<br></div><div><br></div><div><img src="cid:ii_k16eyy3s6" alt="image.png" width="568" height="60"></div><div><br></div><div>Thanks.<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Στις Δευ, 30 Σεπ 2019 στις 3:38 μ.μ., ο/η Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca">cecile.madjar@mcin.ca</a>> έγραψε:<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">Hi Sotirios,<br><div><br></div><div>The StudyUID is stored in the DicomArchiveID field of the tarchive table. It can also be found in the metadata field but it is mixed with many other information.</div><div><br></div><div>Hope this helps,</div><div><br></div><div>Cécile</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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>Hi,</div><div><br></div><div>Is StudyUID stored somewhere at the tables? At the tarchive table, specifically at the AcquisitonMetadata column i found something called 'Unique Study ID" in its context, but that must be the Study Instance UID.</div><div><br></div><div>Thanks<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Στις Παρ, 27 Σεπ 2019 στις 4:22 μ.μ., ο/η Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> έγραψε:<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">Hi Sotirios,<div><br></div><div>Your observation is correct. A little explanation below.<br><div><br></div><div>MINC files get inserted into the MRI violation tables if:</div><div><ul><li>the scan type could not be identified (not matching an entry in the mri_protocol table)</li><li>one parameter of the scan type is out of the expected range present in the mri_protocol_checks (extra filtering in case you need to be stricker on some parameters not present in the mri_protocol table)</li><li>if the CandID and PSCID do not match</li></ul><div>The following cases do not get in the MRI violation tables as it happens before the conversion of the DICOM to MINC files and only MINC files violations are logged there:</div></div><div><ul><li>"No single DICOM" (since no valid DICOM could be found to convert to MINC)</li><li>"Study already inserted" (duplicate StudyUID) since this error happens at the dicomTar.pl level (way before conversion into MINC files)</li></ul><div>Glad everything is working out!!</div></div></div><div>Best,</div><div><br></div><div>Cécile</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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>Hi,</div><div><br></div><div>the mri passed, for some reason it consumed 5.12GB of ram. Now about the mri_violations, dicoms are triggered to be inserted there only if there is a violation for Tr_min, Tr_max, in general for its header parameter? Because i don't see the cases of 'No single dicom" or with the 2 studyiuid to be there. </div><div><br></div><div>Thanks<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Στις Πέμ, 26 Σεπ 2019 στις 5:07 μ.μ., ο/η Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> έγραψε:<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">Hi Sotirios,<div><br></div><div>Sorry to hear you are having issues with the memory. I think most of our VMs are set up with 4GB of RAM so with 4GB you should be fine.</div><div><br></div><div>Hope this helps!</div><div><br></div><div>Cécile</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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>Hi,</div><div><br></div><div>about that dicom that had that insertion error it's about 30mb and when it is being processed the ram is being drastically increased from 2gb to 3.28 and then the whole virtual machine is frozen. What is the recommended size of ram for using Loris?</div><div><br></div><div>Thanks<br></div><div><br></div><div><img src="cid:ii_k10qzt7719" alt="image.png" width="568" height="187"></div><div> <br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Στις Τρί, 24 Σεπ 2019 στις 11:24 μ.μ., ο/η Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> έγραψε:<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">Hi Sotirios,<div><br></div><div>Glad to see that the StudyUID problem was fixed!<br><div><br></div><div>For the delete script issue, if you are absolutely certain that no processes are run for that uploadID, you can update the mri_upload table and set the column <span style="color:rgb(3,47,98);font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre-wrap">Inserting</span> to 0 instead of 1 for that uploadID. It looks like for some reason the scripts did not update this field when it stopped the insertion. Not sure why that would be the case though. </div><div>Note: only do that update if you are certain that there is no processing happening.</div><div><br></div><div>Hope this helps!</div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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>Hi,</div><div><br></div><div>about the Dicoms i reported that didn't have a StudyID they actually do</div><div><div><br></div><div><img src="cid:ii_k0xxqx8817" alt="image.png" width="568" height="66"></div><div><br></div><div><br></div><div><div><img src="cid:ii_k0xxus1619" alt="image.png" width="568" height="21"></div><div><br></div><div>I thought that this might be a permission because "w" was missing at the group. After using chmod -R 775 only 102809579 passed, but with no mnic files. Also now i have this error</div><div><br></div><div>(loris-mri-python) lorisadmin@loris-VirtualBox:/data/loris/bin/mri/tools$ ./<a href="http://delete_imaging_upload.pl" target="_blank">delete_imaging_upload.pl</a> -uploadID 34 -ignore<br>Cannot delete upload 34: the MRI pipeline is currently processing it.<br></div><div><br></div><div>How can solve this?</div><div><br></div><div>Thanks<br></div><div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Στις Τρί, 24 Σεπ 2019 στις 2:30 π.μ., ο/η Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> έγραψε:<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>Hi,</div><div><br></div><div>Here is our auto dicom uploading python script: <a href="https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py" target="_blank">https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py</a></div><div><br></div><div>To give you a brief idea:</div><div>Per folder it will:</div><div>1) Delete all the .bak files</div><div>2) Locate .dcm files and update the Patient header</div><div>3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, TE_max parameters of T1 protocol and do an update at the mri_protocol table <a href="https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205" target="_blank">https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205</a></div><div>For some reason some files are missing SeriesDescription/ProtocolName<br></div><div><br></div><div>In total i have 7 folders</div><div><br></div><div><div><img src="cid:ii_k0x12sox14" alt="image.png" width="568" height="156"></div><div><br></div><div>3/7 passed</div><div><br></div><div><div><img src="cid:ii_k0x13fig15" alt="image.png" width="568" height="198"></div><div><br></div><div>Also about the first patient with DC0000 had a violation "T1 AXIAL SE GADO", but my script didn't output a TE of 17 nowhere and i find that weird since Loris detects the SeriesDescription.<br></div><div><div><img src="cid:ii_k0x14qos16" alt="image.png" width="568" height="143"></div><div><br></div><div><br></div><div>Now about the 4/7 that didn't passed</div><div><br></div><div>102327840 and 102809579 outputs "The target directory does not contain a single DICOM file.", therefore they are missing their StudyUID</div><div><br></div>102506134 has 2 studyuid "You can't use it with data from multiple studies."<div><br></div><div>and 102761034 "No data could be converted into valid MINC files. localizer, scout will not be considered!" What is this?</div><div><br></div><div>If i wanted to force the insertion of 102327840, 102809579 and 102506134 can i just pass a flag parameter to <a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a>? or modify <a href="http://imaging_upload_file.pl" target="_blank">imaging_upload_file.pl</a>?</div><div><br></div><div>Thank you,</div><div><br></div><div>Sotirios<br></div></div></div></div><div><br></div><div>PS</div><div><br></div><div>To diagnose a folder search the name of the folder at dicom_output.txt.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Στις Παρ, 20 Σεπ 2019 στις 4:54 μ.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<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>
<div dir="ltr">Hi Sotirios,
<div>Glad to hear about your progress. </div>
<div><br>
</div>
<div>Yes, the script you used to delete imaging data is <a href="https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md" target="_blank">
fully documented here</a> -- let us know if you didn't find the answers you were looking for there.</div>
<div>(Is it possible the null row in <i>mri_scanner</i> seen in your database management software is a visual placeholder for you as the user? I'm not sure why a scanner would ever be registered with ID='0' as your screenshot showed.)</div>
<div><br>
</div>
<div>Best, </div>
<div>Christine </div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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>I fixed it with this</div>
<div><br>
</div>
<div>
<div><img alt="image.png" width="426" height="36"><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Στις Παρ, 20 Σεπ 2019 στις 4:37 μ.μ., ο/η Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> έγραψε:<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>Hi,</div>
<div><br>
</div>
<div>I tried to create a new candidate using the API, is there something wrong with the structure? why did i receive a 500 internal error? In the loris-error log it state that there is something wrong with token, but i verfied that the type of the token is
a string.<br>
</div>
<div><br>
</div>
<div>[Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client <a href="http://127.0.0.1:59674" target="_blank">
127.0.0.1:59674</a>] PHP Fatal error: Uncaught TypeError: Argument 1 passed to SinglePointLogin::JWTAuthenticate() must be of the type string, null given, called in /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and defined in /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): SinglePointLogin->JWTAuthenticate(NULL)\n#1 /var/www/loris/php/libraries/NDB_Client.class.inc(171): SinglePointLogin->authenticate()\n#2 /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
NDB_Client->initialize('/var/www/loris/...')\n#3 /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): Loris\\API\\APIBase->__construct('POST')\n#4 /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): Loris\\API\\Candidates->__construct('POST', Array)\n#5
{main}\n thrown in /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192<br>
</div>
<div><img alt="image.png" width="568" height="237"><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Στις Παρ, 20 Σεπ 2019 στις 2:39 μ.μ., ο/η Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> έγραψε:<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>Hi,</div>
<div><br>
</div>
<div>Is there a way also to delete candidates? Just to let you know what i did to clear candidates, because maybe i may have missed dependencies.<br>
</div>
<div><br>
</div>
<div>First i deleted all their uploads<br>
./<a href="http://delete_imaging_upload.pl" target="_blank">delete_imaging_upload.pl</a> -uploadID 13 etc ( is there a way to omit the backup file ? )
<br>
<br>
Afterwards i had some scanner candidates, so i deleted all the entries from mri_scanner except that i couldn't delete this entry with the 0 ID.</div>
<div><br>
</div>
<div>
<div><img alt="image.png" width="568" height="251"><br>
</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Lastly i deleted the session and then the candidate table.</div>
<div><br>
</div>
<div>Thanks<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Στις Πέμ, 19 Σεπ 2019 στις 7:57 μ.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<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>
<div dir="ltr">Hi Sotirios,
<div><br>
</div>
<div>We recommend that you use our existing tools for creating new candidates - either the LORIS API or if you are using a PHP script, by calling the
<a href="https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200" target="_blank">
Candidate class's createNew() </a>function. These will create the necessary records for you. (It's not recommended to make direct modifications to mysql database tables in your script, if I understand you.)</div>
<div><br>
</div>
<div>The CandID should be a randomized 6 digit randomized ID, and there are multiple reasons for this. </div>
<div>You can use the PSCID for project-specific IDs and the External ID field in the candidate table can also be used for any values you like. </div>
<div>Additionally, any number of custom IDs can be added in parallel - these are entered/visible in the Candidate Information module and added in the back-end as candidate parameters. </div>
<div><br>
</div>
<div>Best,</div>
<div>Christine </div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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>Hi,</div>
<div><br>
</div>
<div>We are building a script that will auto insert the candidates based on their ExternalID. We would like to know whethere when we are creating a new profile in the candidate table, if we also have to insert a new record at another table? Furthermore is there
a problem that in our case CandID won't be a 6digit? ( should we start it from 100000?)</div>
<div><br>
</div>
<div>Thanks<br>
</div>
<div><br>
</div>
<div>
<div><img alt="image.png" width="414" height="388"></div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Στις Παρ, 13 Σεπ 2019 στις 5:38 μ.μ., ο/η Melanie Legault, Mrs <<a href="mailto:melanie.legault2@mcgill.ca" target="_blank">melanie.legault2@mcgill.ca</a>> έγραψε:<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)">
That would normally be the case but the numeric part of the PSCID get paded with 0 on the left.
<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)">
Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char with a min value of 1, the sequence would be:</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)">
ABC0001<br>
ABC0002</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
...</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
ABC0010</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
...</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)">
thus sorting them ascending will always get the latest value generated as the max value.<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160Signature">
<div id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif">
<p style="margin-top:0px;margin-bottom:0px">M<span>é</span>lanie<br>
</p>
<br>
<p style="margin-top:0px;margin-bottom:0px"></p>
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<div id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160appendonsend">
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160divRplyFwdMsg" dir="ltr">
<font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>><br>
<b>Sent:</b> September 13, 2019 10:15<br>
<b>To:</b> Melanie Legault, Mrs <<a href="mailto:melanie.legault2@mcgill.ca" target="_blank">melanie.legault2@mcgill.ca</a>><br>
<b>Cc:</b> Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>>;
<a href="mailto:loris-dev@bic.mni.mcgill.ca" target="_blank">loris-dev@bic.mni.mcgill.ca</a> <<a href="mailto:loris-dev@bic.mni.mcgill.ca" target="_blank">loris-dev@bic.mni.mcgill.ca</a>><br>
<b>Subject:</b> Re: [Loris-dev] Import mri - scripts</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>I see, although the PSCID value is varchar(255), it must be stored within a specific length of characters. Otherwise if we were to sort strings with different lengths the result would not be sorted correctly ( e.x. 1,2,10,11 as strings would result to
1, 10, 11, 2 ).</div>
<div><br>
</div>
<div>Thanks<br>
</div>
</div>
<br>
<div>
<div dir="ltr">Στις Παρ, 13 Σεπ 2019 στις 4:52 μ.μ., ο/η Melanie Legault, Mrs <<a href="mailto:melanie.legault2@mcgill.ca" target="_blank">melanie.legault2@mcgill.ca</a>> έγραψε:<br>
</div>
<blockquote 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)">
Hello Sotirios,<br>
<br>
There is no `last value` stored anywhere. <br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
The code simply look for the PSCID with the max value and increase that value by 1 in order to generate the next PSCID.</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)">
Hope this info help.<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160x_gmail-m_1788594787074850856Signature">
<div id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160x_gmail-m_1788594787074850856divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif">
<p style="margin-top:0px;margin-bottom:0px">M<span>é</span>lanie Legault <span style="color:rgb(255,0,0)">
|</span> Software developer <span style="color:rgb(255,0,0)">|</span> Faculty of Medicine<span style="color:rgb(255,0,0)"> |</span>
<span style="color:rgb(255,0,0)">McGill University </span> <br>
</p>
<div>3801 University, Montr<span id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160x_gmail-m_1788594787074850856ms-rterangepaste-start"></span><span>é</span><span id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160x_gmail-m_1788594787074850856ms-rterangepaste-end"></span>al,
QC H3A 2B4 </div>
<br>
<p style="margin-top:0px;margin-bottom:0px"></p>
</div>
</div>
<div id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160x_gmail-m_1788594787074850856appendonsend">
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160x_gmail-m_1788594787074850856divRplyFwdMsg" dir="ltr">
<font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b>
<a href="mailto:loris-dev-bounces@bic.mni.mcgill.ca" target="_blank">loris-dev-bounces@bic.mni.mcgill.ca</a> <<a href="mailto:loris-dev-bounces@bic.mni.mcgill.ca" target="_blank">loris-dev-bounces@bic.mni.mcgill.ca</a>> on behalf of Sotirios Nikoloutsopoulos
<<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>><br>
<b>Sent:</b> September 13, 2019 9:43<br>
<b>To:</b> Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>><br>
<b>Cc:</b> <a href="mailto:loris-dev@bic.mni.mcgill.ca" target="_blank">loris-dev@bic.mni.mcgill.ca</a> <<a href="mailto:loris-dev@bic.mni.mcgill.ca" target="_blank">loris-dev@bic.mni.mcgill.ca</a>><br>
<b>Subject:</b> Re: [Loris-dev] Import mri - scripts</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>Hi,</div>
<div><br>
</div>
<div>how does Loris determine the next available PSCID value for a new candidate?
<a href="https://github.com/aces/Loris/wiki/Project-Customization" target="_blank">
https://github.com/aces/Loris/wiki/Project-Customization</a> e.x in the default case the PSCID is sequential, but where do we store the last value for the sequential sequence?<br>
</div>
<div><br>
</div>
<div>Thanks<br>
</div>
</div>
<br>
<div>
<div dir="ltr">Στις Τρί, 10 Σεπ 2019 στις 4:00 π.μ., ο/η Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div>Hi,</div>
<div><br>
</div>
<div>the parameters in the mri_protocol you have assigned are global standard? or were assigned after trial and error?</div>
<div><br>
</div>
<div>Thanks<br>
</div>
</div>
<br>
<div>
<div dir="ltr">Στις Κυρ, 8 Σεπ 2019 στις 10:11 μ.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">Hi Sotirios,
<div><br>
</div>
<div>
<div>Given you have done the initial setup of your tables to match your intended protocol/parameters according to instructions --</div>
</div>
<div>the <a href="https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes" target="_blank">
Troubleshooting guide documentation recommends</a> re-running the pipeline (and first deleting prior uploads). </div>
<div><br>
</div>
<div>Best, </div>
<div>Christine</div>
</div>
<br>
<div>
<div dir="ltr">On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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">*if i were to change their status to resolve what would happen?</div>
<br>
<div>
<div dir="ltr">Στις Κυρ, 8 Σεπ 2019 στις 5:12 μ.μ., ο/η Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div>I noticed that i can view the mnics at the brainbrowser from the mri_violations page ( those mnics are stored at /data/loris/data/trashbin/ if i were to click their issue to resolve what would happend? would they appear in the dicom_archive view too? ).</div>
<div>
<div><br>
</div>
</div>
<div><span id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160x_gmail-m_1788594787074850856x_gmail-m_-3167548388594440731gmail-m_3548729294308866586gmail-m_-7226580865415254747gmail-m_792347981290930428gmail-m_-8197080047898918979gmail-docs-internal-guid-3d4118f8-7fff-7020-bc97-01217b928349" style="font-size:12pt;font-family:"Liberation Mono";color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><span style="border:medium none;display:inline-block;overflow:hidden;width:643px;height:237px"><img style="margin-left: 0px; margin-top: 0px;" src="https://lh5.googleusercontent.com/0G4f5Ms034ZaYEwHLLOzo4YBjQwcKxjSLRrE0XLZAR86JhsPocXi5tkAvgbELadS63HWgJ_A6eGF0BitFWhf4DCVx5EEFzThQm19QfKDpgrrIfGFZjdy4BanrmRjawJeo3kYt-5y" width="643" height="237"></span></span></div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">Στις Κυρ, 8 Σεπ 2019 στις 4:17 μ.μ., ο/η Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div>Hi,</div>
<div><br>
</div>
<div>The defaut values of the schema exists in my local database. If i adjust the default values of TR_min and TE_min the mincs will be uploaded?<br>
</div>
<div><br>
</div>
<div>
<div><img alt="image.png" width="568" height="121"></div>
<div><br>
</div>
<div>
<div><br>
</div>
<div><img alt="image.png" width="549" height="568"></div>
<div><br>
</div>
<div>Thanks<br>
</div>
</div>
</div>
</div>
<br>
<div>
<div dir="ltr">Στις Σάβ, 7 Σεπ 2019 στις 5:48 μ.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">Hi Sotirios,
<div><br>
</div>
<div>Is it possible that you haven't set up your mri_protocol table ? (and mri_scan_type table too, for additional types of scans)</div>
<div><br>
</div>
<div>Like the psc table, this is a pre-requisite for the Imaging insertion setup : See the install/setup documentation : <a href="https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md" target="_blank">https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md</a></div>
<div><br>
</div>
<div>To add new rows, just use MySQL insert statements. You can adapt the insert statements which load the default table values --> e.g. Here on GitHub : <a href="https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718" target="_blank">https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718</a></div>
<div>(see also the mri_scan_type table)</div>
<div><br>
</div>
<div>Best, </div>
<div>Christine</div>
</div>
<br>
<div>
<div dir="ltr">On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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">
<div>I see that i can edit the values but not how to insert new rows.<br>
</div>
<div><br>
</div>
<div><img alt="image.png" width="568" height="266"></div>
<div><br>
</div>
<div>If i choose Inserted with flag then will the minc be inserted?<br>
</div>
<div><br>
</div>
<div>
<div><img alt="image.png" width="284" height="262"><br>
</div>
</div>
</div>
<br>
<div>
<div dir="ltr">Στις Σάβ, 7 Σεπ 2019 στις 3:21 π.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">Hi Sotirios,
<div><br>
</div>
<div>Glad to hear that <i>dcmodify</i> worked correctly. </div>
<div><br>
</div>
<div>For the MRI Violations module, the screenshot is enough. </div>
<div><br>
</div>
<div>It says "could not identify scan type", which we knew already. Did you click on the link on those words? </div>
<div><br>
</div>
<div>It will take you to the next page of the module, showing for each scan what the scan parameters were, and will also show for comparison what's stored in your
<i>mri_protocol</i> table. </div>
<div>Compare these values to find which parameter was not correct according to your
<i>mri_protocol</i> table scan type definitions.</div>
<div><br>
</div>
<div>You may end up broadening your mri_protocol value ranges (e.g. TR, TE) for scans.</div>
<div>This can be done in the front-end, by editing the database table directly in the same subpage of the MRI Violations module.</div>
<div><br>
</div>
<div>The MRI Violations module features are explained in more detail in the Help text for this module inside LORIS (click the ["?"] icon in the menu bar.)</div>
<div><br>
</div>
<div>
<div>See also: <a href="https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md" target="_blank">Loris-MRI troubleshooting guide</a>: <span style="background-color:rgba(27,31,35,0.05);color:rgb(36,41,46);font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:13.6px">no
MINCs inserted</span>- violated scans</div>
</div>
<div><br>
</div>
<div>Best, </div>
<div>Christine </div>
</div>
<br>
<div>
<div dir="ltr">On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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">
<div>Hi,</div>
<div><br>
</div>
<div>looks like my previous email's attachment wasn't delivered due to security reasons, i uploaded my file at google drive
<a href="https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing" target="_blank">
https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing</a></div>
</div>
<br>
<div>
<div dir="ltr">Στις Σάβ, 7 Σεπ 2019 στις 3:02 π.μ., ο/η Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div>Hi,</div>
<div><br>
</div>
<div>From Dicat's view seems that dcmodify worked in both cases</div>
<div><br>
</div>
<div>
<div><img alt="image.png" width="533" height="27"><br>
</div>
</div>
<div>
<div><br>
</div>
<div>
<div><img alt="image.png" width="526" height="30"></div>
<div><br>
</div>
<div>For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier.<br>
</div>
</div>
<div><br>
</div>
<div><img alt="image.png" width="568" height="231"></div>
<div><br>
</div>
<div>Thanks<br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div>
<div dir="ltr">Στις Παρ, 6 Σεπ 2019 στις 7:49 μ.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">Hi Sotirios --
<div>Great, sounds like more progress. </div>
<div><br>
</div>
<div>
<div>About the dcmodify command -- I'm not sure why you're getting an Endian warning. (it's a warning not an error, correct?)</div>
<div>To clarify -- Were the DICOM headers (PatientName) all successfully relabelled, after the command ran? </div>
<div><br>
</div>
<div>You can use also our DICAT tool (<a href="https://github.com/aces/DICAT" target="_blank">https://github.com/aces/DICAT</a>) to verify and/or update local DICOM headers -- though your dcmodify command is a great and fast solution for bulk header updates. </div>
<div><br>
</div>
<div>If you're concerned about fields being changed (e.g. "(2001,105f)" from the warning message) - you can also dcmdump a DICOM slice before and look at these fields specifically. </div>
<div>It's also not a bad "sanity check" to backup your DICOMS before/after running dcmodify, and use dcmdump on each version to diff the outputs -- this will pinpoint what changed. </div>
<div><br>
</div>
<div>Re the protocol violation -- AcquisitionProtocol not recognized or unknown : this means your scans did not match what is stored in your mri_protocol table. </div>
<div>Check the MRI Violations front-end module -- can you see why they didn't match? </div>
<div>Send us an example, in addition to the contents of the mri_protocol table, if you can't find the source of the mismatch. </div>
<div><br>
</div>
<div>Best,</div>
<div>Christine</div>
<div><br>
</div>
</div>
</div>
<br>
<div>
<div dir="ltr">On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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">
<div> Here is the psc table<br>
</div>
<div><img alt="image.png" width="474" height="95"></div>
<div><br>
</div>
<div>I created 2 candidates profiles through the interface<br>
</div>
<div><br>
</div>
<div>
<div><img alt="image.png" width="568" height="114"></div>
<div><br>
</div>
<div>then runned dcmodify command to a dicom file</div>
<div><br>
</div>
<div>dcmodify -ma PatientName="DCC0000_258024_V1" /home/lorisadmin/DICOMS/000535670/501/*.dcm</div>
<div><br>
</div>
<div>and got those warning: is this okay?<br>
</div>
<div>W: Found element (2001,105f) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
W: Found element (2005,1083) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
W: Found element (2005,1402) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
W: Found element (2005,140f) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
W: Found element (2001,105f) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
W: Found element (2005,1083) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246)</div>
</div>
<div><br>
</div>
<div>dcmodify at another Dicom didn't show warnings. Below you can see the execution for the second dicom. Mnics could not be inserted due to AcquisitionProtocol being unknown.</div>
<br>
<div>Running now the following command: /data/loris/bin/mri//uploadNeuroDB/<a href="http://imaging_upload_file.pl" target="_blank">imaging_upload_file.pl</a> -profile prod -upload_id 12 /data/incoming/DCC0001_602102_V1.tar.gz -verbose<br>
<br>
find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' -delete <br>
<br>
dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
<br>
Source: /tmp/ImagingUpload-18-36-mTrxXs<br>
Target: /data/loris/data/tarchive<br>
<br>
Testing for database connectivity.<br>
Database is available.<br>
<br>
You will archive the dir : ImagingUpload-18-36-mTrxXs<br>
<br>
You are creating a tar with the following command:<br>
<br>
tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar ImagingUpload-18-36-mTrxXs<br>
<br>
<br>
getting md5sums and gzipping!!<br>
<br>
* Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs<br>
* Archive target location : /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar<br>
* Name of creating host : 127.0.1.1<br>
* Name of host OS : Linux<br>
* Created by user : lorisadmin<br>
* Archived on : 2019-09-06 18:36:50<br>
* dicomSummary version : 1<br>
* dicomTar version : 1<br>
* md5sum for DICOM tarball : b1dcdc8903dd2d9a5443227db2aa2814 ImagingUpload-18-36-mTrxXs.tar<br>
* md5sum for DICOM tarball gzipped : aeae87f20155a6805f7e0cfe5212ea5f ImagingUpload-18-36-mTrxXs.tar.gz<br>
* md5sum for complete archive : 1d9258d1f077ebc49111ab7ba22a8d6e DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar<br>
<br>
Adding archive info into database<br>
<br>
Removing temporary files from target location<br>
<br>
<br>
Done adding archive info into database<br>
<br>
\/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation -profile prod \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar -uploadID 12 -verbose
<br>
md5sum /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar<br>
PSCID is: DCC0001<br>
CandID id: 602102<br>
visit_label is: V1<br>
PSCID is: DCC0001<br>
CandID id: 602102<br>
visit_label is: V1<br>
candidate id 602102<br>
Set centerID = 1<br>
PSCID is: DCC0001<br>
CandID id: 602102<br>
visit_label is: V1<br>
PSCID is: DCC0001<br>
CandID id: 602102<br>
visit_label is: V1<br>
<br>
Number of MINC files that will be considered for inserting into the database: 2<br>
<br>
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-18-37-31ajWx.log
<br>
PSCID is: DCC0001<br>
CandID id: 602102<br>
visit_label is: V1<br>
PSCID is: DCC0001<br>
CandID id: 602102<br>
visit_label is: V1<br>
candidate id 602102<br>
<br>
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-18-37-fanZFj.log
<br>
PSCID is: DCC0001<br>
CandID id: 602102<br>
visit_label is: V1<br>
PSCID is: DCC0001<br>
CandID id: 602102<br>
visit_label is: V1<br>
candidate id 602102<br>
<br>
Cleaning up temp files: rm -rf /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*<br>
</div>
<div><br>
</div>
<div>(loris-mri-python) lorisadmin@loris-VirtualBox:/data/loris/bin/mri$ cat /data/loris/data/logs/TarLoad-18-37-fanZFj.log
<br>
<br>
==> Loading file from disk /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc<br>
<br>
--> mapping DICOM parameter for /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc<br>
<br>
==> computing md5 hash for MINC body.<br>
<br>
--> md5: 02022dda60d9de429340fec838f50cfe<br>
<br>
==> verifying acquisition protocol<br>
<br>
Acquisition protocol is unknown<br>
<br>
--> The minc file cannot be registered since the AcquisitionProtocol is unknown
<br>
</div>
</div>
<br>
<div>
<div dir="ltr">Στις Τετ, 4 Σεπ 2019 στις 10:46 μ.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">
<div>Hi Sotirios: </div>
<div><br>
</div>
Sure -- you can delete imaging datasets with the <i>delete_imaging_upload</i> script --
<div>details here: <a href="https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md" target="_blank">https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md</a>
<div><br>
</div>
<div>What's in your <i>psc</i> table? (Is it properly populated? <a href="https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database" target="_blank">
This is a pre-requisite to loading imaging data.</a>) </div>
<div>The foreign key constraint error on the candidate record is curious. </div>
<div><br>
</div>
<div>There are also a few options for creating candidates when inserting imaging data:</div>
<div><br>
</div>
<div>-- Method 1 : in 2 steps with the API then DICOM insertion pipeline</div>
<div><br>
</div>
<div>a. via the LORIS API -- Create the candidates (and visits, optionally I think) </div>
<div>How to: <a href="https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api" target="_blank">https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api</a></div>
<div>Ensure you get the DCCID/CandID assigned by LORIS. </div>
<div><br>
</div>
<div>Then as a second step: </div>
<div>b. Use the <a href="https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets" target="_blank">
imaging insertion pipeline</a> to load your DICOMs.</div>
<div>You will want to first ensure that the PatientName header in the DICOMs as well as tar package are correctly labelled with PSCID_DCCID_VisitLabel </div>
<div><br>
</div>
<div>-- Method 2: for BIDS-format datasets: </div>
<div>How to : <a href="https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets" target="_blank">https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets</a></div>
<div><br>
</div>
<div>Be sure to use the <i>-c</i> and <i>-s</i> options when running the <span style="background-color:rgb(246,248,250);color:rgb(36,41,46);font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:13.6px">bids_import</span> script, to
automatically create your candidates and sessions. </div>
<div><br>
</div>
<div>Best, </div>
<div>Christine </div>
</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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>
<div dir="ltr">
<div>How do i delete a Study? And everytime do i have to create a new candidate to get DCCID and a PSCID?</div>
<div><br>
</div>
<div><b>First execution:</b></div>
<div><br>
</div>
<div>(loris-mri-python) lorisadmin@loris-VirtualBox:/data/loris/bin/mri$ ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> -profile prod < ~/Desktop/input.txt > log.txt<br>
Use of uninitialized value $_ in pattern match (m//) at ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> line 144.<br>
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm
line 1060.<br>
ERROR: Failed to insert record in table mri_scanner:<br>
The following database commands failed:<br>
PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';<br>
SET @x1='242126',@x2='Achieva',@x3='3.2.2\3.2.2.0',@x4='34037',@x5='Philips Medical Systems';<br>
EXECUTE s USING @x1,@x2,@x3,@x4,@x5;<br>
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)<br>
<br>
ERROR: The validation has failed. Either re-run the validation again and fix the problem. Or re-run tarchiveLoader.pl using -force to force the execution.<br>
<br>
<br>
The tarchiveLoader.pl insertion script has failed.<br>
Can't exec "mail": No such file or directory at ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> line 249.<br>
print() on closed filehandle MAIL at ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> line 250.<br>
print() on closed filehandle MAIL at ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> line 251.<br>
</div>
<div><br>
</div>
<div><b>And second execution:<br>
</b></div>
<div><br>
</div>
<div>(loris-mri-python) lorisadmin@loris-VirtualBox:/data/loris/bin/mri$ ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> -profile prod < ~/Desktop/input.txt > log.txt</div>
Use of uninitialized value $_ in pattern match (m//) at ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> line 144.<br>
<br>
PROBLEM:<br>
The user 'lorisadmin' has already inserted this study.<br>
The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.<br>
This is the information retained from the first time the study was inserted:<br>
<br>
* Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy<br>
* Archive target location : /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar<br>
* Name of creating host : 127.0.1.1<br>
* Name of host OS : Linux<br>
* Created by user : lorisadmin<br>
* Archived on : 2019-09-04 18:33:05<br>
* dicomSummary version : 1<br>
* dicomTar version : 1<br>
* md5sum for DICOM tarball : 4a301b0318178b09b91e63544282364d ImagingUpload-18-33-Qq7HGy.tar<br>
* md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec ImagingUpload-18-33-Qq7HGy.tar.gz<br>
* md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053 DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar<br>
<br>
<br>
Last update of record:<br>
<br>
<br>
<br>
The dicomTar.pl execution has failed.<br>
Can't exec "mail": No such file or directory at ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> line 249.<br>
print() on closed filehandle MAIL at ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> line 250.<br>
print() on closed filehandle MAIL at ./<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a> line 251.<br>
</div>
<br>
<div>
<div dir="ltr">Στις Τετ, 4 Σεπ 2019 στις 5:35 μ.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">Hi Sotirios,
<div><br>
</div>
<div>Ok, this sounds like good progress. Let us know when you next encounter issues as you progress through the
<a href="https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md" target="_blank">
Imaging Install/Setup docs</a>. </div>
<div>I'll look into how we can better handle the incoming/ directory next time.</div>
<div>Best, </div>
<div>Christine</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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">
<div>/data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is populated correctly except its port is 'port' : ''. Also i have tested that i can connect to MySQL with lorisuser.</div>
<div><br>
</div>
<div>I executed the script again, because the only error i had previously was that the /data/incoming folder didn't exist and there are no errors reported back except of warnings <<mysql: [Warning] Using a password on the command line interface can be insecure>>.<br>
<br>
</div>
</div>
<br>
<div>
<div dir="ltr">Στις Τετ, 4 Σεπ 2019 στις 4:53 μ.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">Hi Sotirios,
<div><br>
</div>
<div>It's possible -- if the script was unable to connect to the database during its execution (e.g. typo in the password), that would explain the underpopulated Image path and Loris-MRI code path you saw in the Config module. </div>
<div>
<div>It's hard to tell without seeing the output from your script run -- Did you see a sign of any such error? </div>
</div>
<div>
<div>The Config fields are populated by the imaging_install.sh script (<a href="https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222" target="_blank">starting at line 222</a>)</div>
</div>
<div><br>
</div>
<div>For example, check if the database connection information was populated accurately in <span style="box-sizing:border-box;color:rgb(36,41,46);font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre-wrap">$mridir</span><span style="color:rgb(36,41,46);font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre-wrap">/dicom-archive/.loris_mri/database_config.py</span></div>
<div><br>
</div>
<div>Best, </div>
<div>Christine </div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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">
<div>Hi Christine,</div>
<div><br>
</div>
<div>If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically?</div>
<div><br>
</div>
<div>Thanks<br>
</div>
<div><br>
</div>
<div><span id="gmail-m_-3093859743545743799gmail-m_-7335306087332203499gmail-m_4327934372587183348gmail-m_9029244433926654390gmail-m_-7112643154635372512gmail-m_555207164701394055gmail-m_-4836309438212291754gmail-m_7388120509628881753gmail-m_-8862036629910070048gmail-m_7504865834240792508gmail-m_7506818949052903434gmail-m_-4521400299788737590gmail-m_-4556282895717094327gmail-m_2208858834862413458gmail-m_-7606483943376083211gmail-m_4685195513250460156gmail-m_4740193449634349544gmail-m_2492866655079990586gmail-m_-6439257914874539744gmail-m_7821434326123037160x_gmail-m_1788594787074850856x_gmail-m_-3167548388594440731gmail-m_3548729294308866586gmail-m_-7226580865415254747gmail-m_792347981290930428gmail-m_-8197080047898918979gmail-m_-7710920244636668843gmail-m_-3002529888196610068gmail-m_-8033494818066357858gmail-m_-2866604804653181673gmail-m_-8620376780104517438gmail-m_9177414638715189166gmail-m_2864429039630937146gmail-m_-5713652945165830627gmail-m_2109631598729112720gmail-m_-8521048869231606025gmail-m_3711759864345043446gmail-m_1992302784649939721gmail-m_7008686204586433049gmail-m_1992294552581681947gmail-m_4598245759171013008gmail-m_-5107689338977711146gmail-m_-8529647138681479763gmail-m_-1465391918538176012gmail-m_-6152858793030714160gmail-m_-8226803066969393218gmail-m_-3978559249485041190gmail-m_-5564460488188384308gmail-docs-internal-guid-493b8c1f-7fff-ca68-b60f-7d41f0b6dd9b" style="border:medium none;display:inline-block;overflow:hidden;width:643px;height:345px"><img style="margin-left: 0px; margin-top: 0px;" src="https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs" width="643" height="345"></span></div>
</div>
<br>
<div>
<div dir="ltr">Στις Τετ, 4 Σεπ 2019 στις 4:16 μ.μ., ο/η Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> έγραψε:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">Hi Sotirios,
<div><br>
</div>
<div>Glad to hear your LORIS core install is up and working and all the front-end pages are loading. </div>
<div><br>
</div>
<div>
<div>> lorisadmin@loris-VirtualBox:/var/www/loris$ chmod 775 project</div>
<div>> and the web interface worked.</div>
</div>
<div><br>
</div>
<div>Yes, it's important that project/ have 775 permissions and that lorisadmin be part of the sudoers group, per
<a href="https://github.com/aces/Loris#install-steps" target="_blank">step 1 in the install Readme</a>. </div>
<div><br>
</div>
<div>
<div>> As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right?<br>
</div>
<br>
</div>
<div>These imaging paths will be updated during <a href="https://github.com/aces/Loris/wiki/Setup" target="_blank">
your imaging installation</a> by an automated script -- you do not need to set them manually via the Config module. </div>
<div>Please continue to follow the <a href="https://github.com/aces/Loris/wiki/Setup" target="_blank">
Setup Guide</a> for detailed steps to follow.</div>
<div><br>
</div>
<div>Best, </div>
<div>Christine </div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
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<br>
<div>
<div dir="ltr">On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@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">
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<div>As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right?<br>
</div>
<div><br>
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<div><img alt="image.png" width="474" height="332"></div>
<div><br>
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<br>
<div>
<div dir="ltr">Στις Τετ, 4 Σεπ 2019 στις 2:28 μ.μ., ο/η Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> έγραψε:<br>
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<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div>Hi,</div>
<div><br>
</div>
<div>i used</div>
<div><br>
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<div>
<pre style="box-sizing:border-box;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:11.9px;margin-bottom:16px;margin-top:0px;background-color:rgb(246,248,250);border-radius:3px;line-height:1.45;overflow:auto;padding:16px;color:rgb(36,41,46)"><code style="box-sizing:border-box;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:11.9px;background:transparent none repeat scroll 0% 0%;border-radius:3px;margin:0px;padding:0px;border:0px none;word-break:normal;display:inline;line-height:inherit;overflow:visible">curl -sL <a href="https://deb.nodesource.com/setup_8.x" target="_blank">https://deb.nodesource.com/setup_8.x</a> | sudo -E bash -
sudo apt-get install -y <span>nodejs<br><br></span></code></pre>
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<div><br>
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<div>you had suggested in the past, make worked and now i can see all the contents in the web-interface, but i don't need make install?</div>
<div><br>
</div>
<div>Thanks<br>
</div>
</div>
</blockquote>
</div>
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<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
McGill Centre for Integrative Neuroscience | MCIN.ca</div>
<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
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<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
McGill Centre for Integrative Neuroscience | MCIN.ca</div>
<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
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<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
McGill Centre for Integrative Neuroscience | MCIN.ca</div>
<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
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<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
McGill Centre for Integrative Neuroscience | MCIN.ca</div>
<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
</div>
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McGill Centre for Integrative Neuroscience | MCIN.ca</div>
<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
</div>
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</div>
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<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
McGill Centre for Integrative Neuroscience | MCIN.ca</div>
<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
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<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
McGill Centre for Integrative Neuroscience | MCIN.ca</div>
<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
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McGill Centre for Integrative Neuroscience | MCIN.ca</div>
<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
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McGill Centre for Integrative Neuroscience | MCIN.ca</div>
<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
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<div>Montreal Neurological Institute</div>
<div>McGill University | Montreal | Canada</div>
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