<div dir="ltr">Hi Sotirios,<div><br></div><div>I took a closer look to the batch_uploader_multiple_output.txt file you sent. It looks like there are different reasons for failure depending on the DICOM folder uploaded.</div><div><ul><li>For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 V1: it looks like there is no file of type DICOM in the folder. Have you checked to see if that is indeed the case? Maybe you can try running the following command on that folder to see what are the types of the files? If it does not return at least one DICOM medical imaging data file, then that is why you get the error message from the pipeline:</li><ul><li><pre style="box-sizing:inherit;margin-top:0px;margin-bottom:0px;padding:0px 4px;font-size:13px;line-height:inherit;font-variant-ligatures:contextual;white-space:pre-wrap;word-break:normal;font-family:inherit;border-width:0px;border-radius:0px;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;color:rgb(29,28,29);overflow:visible">find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq</pre></li></ul><li><font color="#1d1c1d"><span style="font-variant-ligatures:contextual;white-space:pre-wrap">For </span></font>864173 DCC0001 V1: it looks like there are two different DICOM studies within the same folder. You will need to split that study in two based on the StudyUID field as the insertion pipeline does not allow for more than one StudyUID per upload.<br></li><li>For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 V1: it looks like the dcm2mnc command did not produce any MINC files. Can you check in the DICOM archive what are the series present in the tarchive for that visit? Maybe only a scout or localizer was acquired for that session, hence the no valid MINC files (scout and localizer being skipped for the conversion)</li><li>For 397410 DCC0003 V1: it looks like everything went well for this one.</li></ul><div>One script that is called by our pipeline is called <a href="http://get_dicom_info.pl">get_dicom_info.pl</a> and this does all kind of checks on the DICOM files (it is being called when running the dcm2mnc conversion). You could run it independently on your folder if needed.</div></div><div><br></div><div>Since one of the study got in, it does not look like you are having a problem with the setup. It seems more likely to be a problem with the data themselves.</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 Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com">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 Christine,</div><div><br></div><div>In my first vm i am able to create the minc files and view them at the mri browser (except of candidate 102761034 ), meanwhile the same files gives warnings at the 2nd vm. The output of the batch upload can be seen in the file attached. <br></div><div>Also a colleague of us has built a pre-validation tool for dicom <a href="https://github.com/aueb-wim/DataQualityControlTool/" target="_blank">https://github.com/aueb-wim/DataQualityControlTool/</a> which had found all the files that Loris gave as warning . Basically I confirmed that the total amount of files per dicom was the same amount as stated in Loris and checked some filenames given from warning to confirm that they match with our tool. But that was months ago and my colleague had changed some parameters for MIP and now our tool doesn't find all the invalid files, that's why i asked for the dicom header specification of Loris. In a discussion we had he mentioned that he doesn't check for some tags e.x. orientation. Lastly to mention that in my first vm i didn't use our tool to remove invalid dcm files.<br></div><div><br></div><div>Thanks<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Στις Τετ, 13 Νοε 2019 στις 11:45 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>Can you provide us with some fresh particulars of the current issue and we'll take it from there? </div>
<div>Yang's team has built these scripts which can definitely serve as a model for your pre-validation of your DICOM collections. </div>
<div>cheers, </div>
<div>Christine </div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Nov 13, 2019 at 4:23 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 Yang,</div>
<div><br>
</div>
<div>We make use of pydicom library too. Now about the validate.py i see that you check if some attributes are missing such as PatientID, PatientName which all of our files contains that info. Maybe i have missed something on the setup of my other virtual machine
( although one dicom passed on the new vm successfully, the others that were inserted correctly on my old vm fails on the new one ), i think that i had asked about this error "Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/<a href="http://batch_uploads_imageuploader.pl" target="_blank">batch_uploads_imageuploader.pl</a>
line 144." but i don't remember the solution.</div>
<div><br>
</div>
<div>Thanks<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Στις Τετ, 13 Νοε 2019 στις 5:45 π.μ., ο/η Yang Ding <<a href="mailto:it@cnbp.ca" target="_blank">it@cnbp.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>Hey, Sotirios,</div>
<div><br>
</div>
<div>Christine from the LORIS team mentioned you had some issue with DICOM. I am a fellow developer for an external project using LORIS, kind of just like you. We had to implement DICOM upload as well but more as a fully automated pipeline actually. </div>
<div><br>
</div>
<div>While we were building CNBP, we had coded up some minor Python functions to check DICOM integrity (and simple validations) and you might be able to gain some inspiration from it and help you with your cause. For more comprehensive solution, PyDICOM (<a href="https://pydicom.github.io/pydicom/stable/getting_started.html#" target="_blank">https://pydicom.github.io/pydicom/stable/getting_started.html#</a>) seems
like a descent python package to help out with a lot of DICOM data checks (I was essentially just building customized wrapper calls to them). You can see some example scripts here as part of our DICOM submodule. It is pretty rough around the edges but hopefully
point you in the right direcitons <a href="https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py" target="_blank">https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py</a></div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Yang Ding, PhD. </div>
<div>Canadian Neonatal Brain Platform Architect</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Nov 12, 2019 at 8:29 AM <<a href="mailto:loris-dev-request@bic.mni.mcgill.ca" target="_blank">loris-dev-request@bic.mni.mcgill.ca</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Today's Topics:<br>
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1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 12 Nov 2019 15:28:26 +0200<br>
From: Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>><br>
To: Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>><br>
Cc: <a href="mailto:loris-dev@bic.mni.mcgill.ca" target="_blank">loris-dev@bic.mni.mcgill.ca</a><br>
Subject: Re: [Loris-dev] Import mri - scripts<br>
Message-ID:<br>
<CAKHj7uST=<a href="mailto:92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ@mail.gmail.com" target="_blank">92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
<br>
Could we send you a link with 10 anonymized dicom files to diagnose the<br>
warnings we get?<br>
<br>
Thanks<br>
<br>
???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
<br>
> Hi Cecile,<br>
><br>
> We were wondering whether Loris has a tool to check if there are problems<br>
> with the dcm files, before trying to upload them. Something that could<br>
> provide the same results provided in the warning_output, this is the<br>
> summary from the mri_upload at the front-page. Also which attributes of the<br>
> dcm header would trigger a warning? is there a dcm file header<br>
> specification for Loris?<br>
><br>
> Thanks<br>
><br>
> Sotirios<br>
><br>
> ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
><br>
>> Hi,<br>
>><br>
>> Yes, by parsing now() into unix_timestamp function it worked,but i<br>
>> thought that something else was causing the 2nd issue.<br>
>> Thanks<br>
>><br>
>> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, <<br>
>> <a href="mailto:xavier.lecoursboucher@mcgill.ca" target="_blank">xavier.lecoursboucher@mcgill.ca</a>> wrote:<br>
>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> The first error occurs because the QCFirstChangeTime and columns are of<br>
>>> type `unsigned integer` and not `datatime`. You should be using<br>
>>> UNIX_TIMESTAMP() instead of NOW().<br>
>>><br>
>>> The second error occurs because the trigger triggers a rollback of the<br>
>>> insert statement in the files table.<br>
>>> See mysql documentation for trigger error handling.<br>
>>><br>
>>> An error during either a BEFORE or AFTER trigger results in failure of<br>
>>> the entire statement that caused trigger invocation.<br>
>>><br>
>>><br>
>>> Thank you for sharing that. I hope it helps.<br>
>>> -- Xavier<br>
>>><br>
>>> ------------------------------<br>
>>> *From:* <a href="mailto:loris-dev-bounces@bic.mni.mcgill.ca" target="_blank">
loris-dev-bounces@bic.mni.mcgill.ca</a> <<br>
>>> <a href="mailto:loris-dev-bounces@bic.mni.mcgill.ca" target="_blank">loris-dev-bounces@bic.mni.mcgill.ca</a>> on behalf of Sotirios<br>
>>> Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>><br>
>>> *Sent:* October 1, 2019 8:33 AM<br>
>>> *To:* Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>><br>
>>> *Cc:* <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>
>>> Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>><br>
>>> *Subject:* Re: [Loris-dev] Import mri - scripts<br>
>>><br>
>>> When mincs are inserted their corresponding rows at the file table are<br>
>>> inserted too<br>
>>> [image: image.png]<br>
>>><br>
>>> i would like to insert their rows at file_qcstatus as well, because i<br>
>>> don't want manually to label them as passed throught the interface<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>><br>
>>> That is the trigger i wrote<br>
>>><br>
>>> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` AFTER<br>
>>> INSERT ON `files` FOR EACH ROW<br>
>>> BEGIN<br>
>>> INSERT INTO files_qcstatus<br>
>>> SET FileID = NEW.FileID,<br>
>>> SeriesUID = NEW.SeriesUID,<br>
>>> EchoTime = NEW.EchoTime,<br>
>>> QCStatus = "Pass",<br>
>>> QCFirstChangeTime = NOW(),<br>
>>> QCLastChangeTime = NOW();<br>
>>> END<br>
>>><br>
>>> although it contains some errors<br>
>>><br>
>>> DBD::mysql::db do failed: Out of range value for column<br>
>>> 'QCFirstChangeTime' at row 1 at<br>
>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.<br>
>>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign<br>
>>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT<br>
>>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`))<br>
>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar <<br>
>>> <a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> In the mri_upload table, there is a TarchiveID column associated with<br>
>>> the MRI upload you inserted. When this value is NULL, it means no DICOMs<br>
>>> were inserted into the tarchive tables. At the end of the insertion of the<br>
>>> DICOMs in the tarchive tables, this value is updated with the correct<br>
>>> TarchiveID associated with the upload.<br>
>>><br>
>>> Could this correspond to what you want to do?<br>
>>><br>
>>> Regarding the files_qcstatus, this table is only linked to the files<br>
>>> table (hence, the MINC files). You could always create a new table for<br>
>>> dicom_qcstatus and link it to the tarchive table?<br>
>>><br>
>>> C?cile<br>
>>><br>
>>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> i would like whenever a dicom is imported to mark all their<br>
>>> coressponding qc_status to "pass". I was thinking of creating a trigger for<br>
>>> that, but which tables do i need to add entries to? So far from what i see<br>
>>> i need to add entres at the table "files" whenever an insertion happens to<br>
>>> files_qcstatus.<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> Oh, sorry i should have asked for StudyID, at the beginning of my email<br>
>>> i sent 3 hours ago (not StudyUID).<br>
>>><br>
>>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> that's the Study Instance UID, not the StudyID. So the StudyID i am<br>
>>> looking for is not stored in the database?<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> Thanks.<br>
>>><br>
>>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar <<br>
>>> <a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> The StudyUID is stored in the DicomArchiveID field of the<br>
>>> tarchive table. It can also be found in the metadata field but it is mixed<br>
>>> with many other information.<br>
>>><br>
>>> Hope this helps,<br>
>>><br>
>>> C?cile<br>
>>><br>
>>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> Is StudyUID stored somewhere at the tables? At the tarchive table,<br>
>>> specifically at the AcquisitonMetadata column i found something called<br>
>>> 'Unique Study ID" in its context, but that must be the Study Instance UID.<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar <<br>
>>> <a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> Your observation is correct. A little explanation below.<br>
>>><br>
>>> MINC files get inserted into the MRI violation tables if:<br>
>>><br>
>>> - the scan type could not be identified (not matching an entry in<br>
>>> the mri_protocol table)<br>
>>> - one parameter of the scan type is out of the expected range<br>
>>> present in the mri_protocol_checks (extra filtering in case you need to be<br>
>>> stricker on some parameters not present in the mri_protocol table)<br>
>>> - if the CandID and PSCID do not match<br>
>>><br>
>>> The following cases do not get in the MRI violation tables as it happens<br>
>>> before the conversion of the DICOM to MINC files and only MINC files<br>
>>> violations are logged there:<br>
>>><br>
>>> - "No single DICOM" (since no valid DICOM could be found to convert<br>
>>> to MINC)<br>
>>> - "Study already inserted" (duplicate StudyUID) since this error<br>
>>> happens at the dicomTar.pl level (way before conversion into MINC files)<br>
>>><br>
>>> Glad everything is working out!!<br>
>>> Best,<br>
>>><br>
>>> C?cile<br>
>>><br>
>>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> the mri passed, for some reason it consumed 5.12GB of ram. Now about the<br>
>>> mri_violations, dicoms are triggered to be inserted there only if there is<br>
>>> a violation for Tr_min, Tr_max, in general for its header parameter?<br>
>>> Because i don't see the cases of 'No single dicom" or with the 2 studyiuid<br>
>>> to be there.<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar <<br>
>>> <a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> Sorry to hear you are having issues with the memory. I think most of our<br>
>>> VMs are set up with 4GB of RAM so with 4GB you should be fine.<br>
>>><br>
>>> Hope this helps!<br>
>>><br>
>>> C?cile<br>
>>><br>
>>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> about that dicom that had that insertion error it's about 30mb and when<br>
>>> it is being processed the ram is being drastically increased from 2gb to<br>
>>> 3.28 and then the whole virtual machine is frozen. What is the recommended<br>
>>> size of ram for using Loris?<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>><br>
>>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar <<br>
>>> <a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> Glad to see that the StudyUID problem was fixed!<br>
>>><br>
>>> For the delete script issue, if you are absolutely certain that no<br>
>>> processes are run for that uploadID, you can update the mri_upload table<br>
>>> and set the column Inserting to 0 instead of 1 for that uploadID. It<br>
>>> looks like for some reason the scripts did not update this field when it<br>
>>> stopped the insertion. Not sure why that would be the case though.<br>
>>> Note: only do that update if you are certain that there is no processing<br>
>>> happening.<br>
>>><br>
>>> Hope this helps!<br>
>>><br>
>>><br>
>>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> about the Dicoms i reported that didn't have a StudyID they actually do<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> I thought that this might be a permission because "w" was missing at the<br>
>>> group. After using chmod -R 775 only 102809579 passed, but with no mnic<br>
>>> files. Also now i have this error<br>
>>><br>
>>> (loris-mri-python) lorisadmin@loris-VirtualBox:/data/loris/bin/mri/tools$<br>
>>> ./<a href="http://delete_imaging_upload.pl" rel="noreferrer" target="_blank">delete_imaging_upload.pl</a> -uploadID 34 -ignore<br>
>>> Cannot delete upload 34: the MRI pipeline is currently processing it.<br>
>>><br>
>>> How can solve this?<br>
>>><br>
>>> Thanks<br>
>>><br>
>>><br>
>>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> Here is our auto dicom uploading python script:<br>
>>> <a href="https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py" rel="noreferrer" target="_blank">
https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py</a><br>
>>><br>
>>> To give you a brief idea:<br>
>>> Per folder it will:<br>
>>> 1) Delete all the .bak files<br>
>>> 2) Locate .dcm files and update the Patient header<br>
>>> 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min,<br>
>>> TE_max parameters of T1 protocol and do an update at the mri_protocol table<br>
>>> <a href="https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205" rel="noreferrer" target="_blank">
https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205</a><br>
>>> For some reason some files are missing SeriesDescription/ProtocolName<br>
>>><br>
>>> In total i have 7 folders<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> 3/7 passed<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> Also about the first patient with DC0000 had a violation "T1 AXIAL SE<br>
>>> GADO", but my script didn't output a TE of 17 nowhere and i find that weird<br>
>>> since Loris detects the SeriesDescription.<br>
>>> [image: image.png]<br>
>>><br>
>>><br>
>>> Now about the 4/7 that didn't passed<br>
>>><br>
>>> 102327840 and 102809579 outputs "The target directory does not contain a<br>
>>> single DICOM file.", therefore they are missing their StudyUID<br>
>>><br>
>>> 102506134 has 2 studyuid "You can't use it with data from multiple<br>
>>> studies."<br>
>>><br>
>>> and 102761034 "No data could be converted into valid MINC files.<br>
>>> localizer, scout will not be considered!" What is this?<br>
>>><br>
>>> If i wanted to force the insertion of 102327840, 102809579 and 102506134<br>
>>> can i just pass a flag parameter to <a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">
batch_uploads_imageuploader.pl</a>? or<br>
>>> modify <a href="http://imaging_upload_file.pl" rel="noreferrer" target="_blank">
imaging_upload_file.pl</a>?<br>
>>><br>
>>> Thank you,<br>
>>><br>
>>> Sotirios<br>
>>><br>
>>> PS<br>
>>><br>
>>> To diagnose a folder search the name of the folder at dicom_output.txt.<br>
>>><br>
>>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>> Glad to hear about your progress.<br>
>>><br>
>>> Yes, the script you used to delete imaging data is fully documented here<br>
>>> <<a href="https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md" rel="noreferrer" target="_blank">https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md</a>><br>
>>> -- let us know if you didn't find the answers you were looking for there.<br>
>>> (Is it possible the null row in *mri_scanner* seen in your database<br>
>>> management software is a visual placeholder for you as the user? I'm not<br>
>>> sure why a scanner would ever be registered with ID='0' as your screenshot<br>
>>> showed.)<br>
>>><br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> I fixed it with this<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> I tried to create a new candidate using the API, is there something<br>
>>> wrong with the structure? why did i receive a 500 internal error? In the<br>
>>> loris-error log it state that there is something wrong with token, but i<br>
>>> verfied that the type of the token is a string.<br>
>>><br>
>>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client<br>
>>> <a href="http://127.0.0.1:59674" rel="noreferrer" target="_blank">127.0.0.1:59674</a>] PHP Fatal error: Uncaught TypeError: Argument 1<br>
>>> passed to SinglePointLogin::JWTAuthenticate() must be of the type string,<br>
>>> null given, called in<br>
>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and<br>
>>> defined in<br>
>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack<br>
>>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):<br>
>>> SinglePointLogin->JWTAuthenticate(NULL)\n#1<br>
>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):<br>
>>> SinglePointLogin->authenticate()\n#2<br>
>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):<br>
>>> NDB_Client->initialize('/var/www/loris/...')\n#3<br>
>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):<br>
>>> Loris\\API\\APIBase->__construct('POST')\n#4<br>
>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):<br>
>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in<br>
>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> Is there a way also to delete candidates? Just to let you know what i<br>
>>> did to clear candidates, because maybe i may have missed dependencies.<br>
>>><br>
>>> First i deleted all their uploads<br>
>>> ./<a href="http://delete_imaging_upload.pl" rel="noreferrer" target="_blank">delete_imaging_upload.pl</a> -uploadID 13 etc ( is there a way to omit<br>
>>> the backup file ? )<br>
>>><br>
>>> Afterwards i had some scanner candidates, so i deleted all the entries<br>
>>> from mri_scanner except that i couldn't delete this entry with the 0 ID.<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>><br>
>>> Lastly i deleted the session and then the candidate table.<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> We recommend that you use our existing tools for creating new candidates<br>
>>> - either the LORIS API or if you are using a PHP script, by calling the Candidate<br>
>>> class's createNew()<br>
>>> <<a href="https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200" rel="noreferrer" target="_blank">https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200</a>>function.<br>
>>> These will create the necessary records for you. (It's not recommended to<br>
>>> make direct modifications to mysql database tables in your script, if I<br>
>>> understand you.)<br>
>>><br>
>>> The CandID should be a randomized 6 digit randomized ID, and there are<br>
>>> multiple reasons for this.<br>
>>> You can use the PSCID for project-specific IDs and the External ID field<br>
>>> in the candidate table can also be used for any values you like.<br>
>>> Additionally, any number of custom IDs can be added in parallel - these<br>
>>> are entered/visible in the Candidate Information module and added in the<br>
>>> back-end as candidate parameters.<br>
>>><br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>><br>
>>><br>
>>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> We are building a script that will auto insert the candidates based on<br>
>>> their ExternalID. We would like to know whethere when we are creating a new<br>
>>> profile in the candidate table, if we also have to insert a new record at<br>
>>> another table? Furthermore is there a problem that in our case CandID won't<br>
>>> be a 6digit? ( should we start it from 100000?)<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>><br>
>>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs <<br>
>>> <a href="mailto:melanie.legault2@mcgill.ca" target="_blank">melanie.legault2@mcgill.ca</a>> ??????:<br>
>>><br>
>>> That would normally be the case but the numeric part of the PSCID get<br>
>>> paded with 0 on the left.<br>
>>><br>
>>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char<br>
>>> with a min value of 1, the sequence would be:<br>
>>><br>
>>> ABC0001<br>
>>> ABC0002<br>
>>> ...<br>
>>> ABC0010<br>
>>> ...<br>
>>><br>
>>> thus sorting them ascending will always get the latest value generated<br>
>>> as the max value.<br>
>>><br>
>>> M?lanie<br>
>>><br>
>>> ------------------------------<br>
>>> *From:* Sotirios Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>><br>
>>> *Sent:* September 13, 2019 10:15<br>
>>> *To:* Melanie Legault, Mrs <<a href="mailto:melanie.legault2@mcgill.ca" target="_blank">melanie.legault2@mcgill.ca</a>><br>
>>> *Cc:* Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>>;<br>
>>> <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>
>>> *Subject:* Re: [Loris-dev] Import mri - scripts<br>
>>><br>
>>> I see, although the PSCID value is varchar(255), it must be stored<br>
>>> within a specific length of characters. Otherwise if we were to sort<br>
>>> strings with different lengths the result would not be sorted correctly (<br>
>>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ).<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs <<br>
>>> <a href="mailto:melanie.legault2@mcgill.ca" target="_blank">melanie.legault2@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hello Sotirios,<br>
>>><br>
>>> There is no `last value` stored anywhere.<br>
>>> The code simply look for the PSCID with the max value and increase that<br>
>>> value by 1 in order to generate the next PSCID.<br>
>>><br>
>>> Hope this info help.<br>
>>><br>
>>> M?lanie Legault | Software developer | Faculty of Medicine | McGill<br>
>>> University<br>
>>> 3801 University, Montr?al, QC H3A 2B4<br>
>>><br>
>>> ------------------------------<br>
>>> *From:* <a href="mailto:loris-dev-bounces@bic.mni.mcgill.ca" target="_blank">
loris-dev-bounces@bic.mni.mcgill.ca</a> <<br>
>>> <a href="mailto:loris-dev-bounces@bic.mni.mcgill.ca" target="_blank">loris-dev-bounces@bic.mni.mcgill.ca</a>> on behalf of Sotirios<br>
>>> Nikoloutsopoulos <<a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>><br>
>>> *Sent:* September 13, 2019 9:43<br>
>>> *To:* Christine Rogers, Ms. <<a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>><br>
>>> *Cc:* <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>
>>> *Subject:* Re: [Loris-dev] Import mri - scripts<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> how does Loris determine the next available PSCID value for a new<br>
>>> candidate? <a href="https://github.com/aces/Loris/wiki/Project-Customization" rel="noreferrer" target="_blank">
https://github.com/aces/Loris/wiki/Project-Customization</a><br>
>>> e.x in the default case the PSCID is sequential, but where do we store the<br>
>>> last value for the sequential sequence?<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> the parameters in the mri_protocol you have assigned are global<br>
>>> standard? or were assigned after trial and error?<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> Given you have done the initial setup of your tables to match your<br>
>>> intended protocol/parameters according to instructions --<br>
>>> the Troubleshooting guide documentation recommends<br>
>>> <<a href="https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes" rel="noreferrer" target="_blank">https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes</a>><br>
>>> re-running the pipeline (and first deleting prior uploads).<br>
>>><br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> *if i were to change their status to resolve what would happen?<br>
>>><br>
>>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> I noticed that i can view the mnics at the brainbrowser from the<br>
>>> mri_violations page ( those mnics are stored at /data/loris/data/trashbin/<br>
>>> if i were to click their issue to resolve what would happend? would they<br>
>>> appear in the dicom_archive view too? ).<br>
>>><br>
>>><br>
>>><br>
>>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> The defaut values of the schema exists in my local database. If i adjust<br>
>>> the default values of TR_min and TE_min the mincs will be uploaded?<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> Is it possible that you haven't set up your mri_protocol table ? (and<br>
>>> mri_scan_type table too, for additional types of scans)<br>
>>><br>
>>> Like the psc table, this is a pre-requisite for the Imaging insertion<br>
>>> setup : See the install/setup documentation :<br>
>>> <a href="https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md" rel="noreferrer" target="_blank">
https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md</a><br>
>>><br>
>>> To add new rows, just use MySQL insert statements. You can adapt the<br>
>>> insert statements which load the default table values --> e.g. Here on<br>
>>> GitHub :<br>
>>> <a href="https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718" rel="noreferrer" target="_blank">
https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718</a><br>
>>> (see also the mri_scan_type table)<br>
>>><br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> I see that i can edit the values but not how to insert new rows.<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> If i choose Inserted with flag then will the minc be inserted?<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> Glad to hear that *dcmodify* worked correctly.<br>
>>><br>
>>> For the MRI Violations module, the screenshot is enough.<br>
>>><br>
>>> It says "could not identify scan type", which we knew already. Did you<br>
>>> click on the link on those words?<br>
>>><br>
>>> It will take you to the next page of the module, showing for each scan<br>
>>> what the scan parameters were, and will also show for comparison what's<br>
>>> stored in your *mri_protocol* table.<br>
>>> Compare these values to find which parameter was not correct according<br>
>>> to your *mri_protocol* table scan type definitions.<br>
>>><br>
>>> You may end up broadening your mri_protocol value ranges (e.g. TR, TE)<br>
>>> for scans.<br>
>>> This can be done in the front-end, by editing the database table<br>
>>> directly in the same subpage of the MRI Violations module.<br>
>>><br>
>>> The MRI Violations module features are explained in more detail in the<br>
>>> Help text for this module inside LORIS (click the ["?"] icon in the menu<br>
>>> bar.)<br>
>>><br>
>>> See also: Loris-MRI troubleshooting guide<br>
>>> <<a href="https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md" rel="noreferrer" target="_blank">https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md</a>><br>
>>> : no MINCs inserted- violated scans<br>
>>><br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> looks like my previous email's attachment wasn't delivered due to<br>
>>> security reasons, i uploaded my file at google drive<br>
>>> <a href="https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing" rel="noreferrer" target="_blank">
https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing</a><br>
>>><br>
>>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> From Dicat's view seems that dcmodify worked in both cases<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> For the mri_violations i attached the .html output from webbrowser, so<br>
>>> that you can check the filelds easier.<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> Thanks<br>
>>><br>
>>><br>
>>><br>
>>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios --<br>
>>> Great, sounds like more progress.<br>
>>><br>
>>> About the dcmodify command -- I'm not sure why you're getting an Endian<br>
>>> warning. (it's a warning not an error, correct?)<br>
>>> To clarify -- Were the DICOM headers (PatientName) all successfully<br>
>>> relabelled, after the command ran?<br>
>>><br>
>>> You can use also our DICAT tool (<a href="https://github.com/aces/DICAT" rel="noreferrer" target="_blank">https://github.com/aces/DICAT</a>) to<br>
>>> verify and/or update local DICOM headers -- though your dcmodify command is<br>
>>> a great and fast solution for bulk header updates.<br>
>>><br>
>>> If you're concerned about fields being changed (e.g. "(2001,105f)" from<br>
>>> the warning message) - you can also dcmdump a DICOM slice before and look<br>
>>> at these fields specifically.<br>
>>> It's also not a bad "sanity check" to backup your DICOMS before/after<br>
>>> running dcmodify, and use dcmdump on each version to diff the outputs --<br>
>>> this will pinpoint what changed.<br>
>>><br>
>>> Re the protocol violation -- AcquisitionProtocol not recognized or<br>
>>> unknown : this means your scans did not match what is stored in your<br>
>>> mri_protocol table.<br>
>>> Check the MRI Violations front-end module -- can you see why they didn't<br>
>>> match?<br>
>>> Send us an example, in addition to the contents of the mri_protocol<br>
>>> table, if you can't find the source of the mismatch.<br>
>>><br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>><br>
>>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> Here is the psc table<br>
>>> [image: image.png]<br>
>>><br>
>>> I created 2 candidates profiles through the interface<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>> then runned dcmodify command to a dicom file<br>
>>><br>
>>> dcmodify -ma PatientName="DCC0000_258024_V1"<br>
>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm<br>
>>><br>
>>> and got those warning: is this okay?<br>
>>> W: Found element (2001,105f) with VR UN and undefined length, reading a<br>
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
>>> W: Found element (2005,1083) with VR UN and undefined length, reading a<br>
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
>>> W: Found element (2005,1402) with VR UN and undefined length, reading a<br>
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
>>> W: Found element (2005,140f) with VR UN and undefined length, reading a<br>
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
>>> W: Found element (2001,105f) with VR UN and undefined length, reading a<br>
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
>>> W: Found element (2005,1083) with VR UN and undefined length, reading a<br>
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)<br>
>>><br>
>>> dcmodify at another Dicom didn't show warnings. Below you can see the<br>
>>> execution for the second dicom. Mnics could not be inserted due to<br>
>>> AcquisitionProtocol being unknown.<br>
>>><br>
>>> Running now the following command: /data/loris/bin/mri//uploadNeuroDB/<br>
>>> <a href="http://imaging_upload_file.pl" rel="noreferrer" target="_blank">imaging_upload_file.pl</a> -profile prod -upload_id 12<br>
>>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose<br>
>>><br>
>>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'<br>
>>> -delete<br>
>>><br>
>>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs<br>
>>> \/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<br>
>>> 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 :<br>
>>> /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<br>
>>> ImagingUpload-18-36-mTrxXs.tar<br>
>>> * md5sum for DICOM tarball gzipped : aeae87f20155a6805f7e0cfe5212ea5f<br>
>>> ImagingUpload-18-36-mTrxXs.tar.gz<br>
>>> * md5sum for complete archive : 1d9258d1f077ebc49111ab7ba22a8d6e<br>
>>> 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<br>
>>> -profile prod<br>
>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar<br>
>>> -uploadID 12 -verbose<br>
>>> md5sum<br>
>>> /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<br>
>>> database: 2<br>
>>><br>
>>> log dir is /data/loris/data//logs and log file is<br>
>>> /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<br>
>>> /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<br>
>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*<br>
>>><br>
>>> (loris-mri-python) lorisadmin@loris-VirtualBox:/data/loris/bin/mri$ cat<br>
>>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log<br>
>>><br>
>>> ==> Loading file from disk<br>
>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc<br>
>>><br>
>>> --> mapping DICOM parameter for<br>
>>> /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<br>
>>> is unknown<br>
>>><br>
>>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios:<br>
>>><br>
>>> Sure -- you can delete imaging datasets with the *delete_imaging_upload*<br>
>>> script --<br>
>>> details here:<br>
>>> <a href="https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md" rel="noreferrer" target="_blank">
https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md</a><br>
>>><br>
>>> What's in your *psc* table? (Is it properly populated? This is a<br>
>>> pre-requisite to loading imaging data.<br>
>>> <<a href="https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database" rel="noreferrer" target="_blank">https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database</a>><br>
>>> )<br>
>>> The foreign key constraint error on the candidate record is curious.<br>
>>><br>
>>> There are also a few options for creating candidates when inserting<br>
>>> imaging data:<br>
>>><br>
>>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline<br>
>>><br>
>>> a. via the LORIS API -- Create the candidates (and visits, optionally I<br>
>>> think)<br>
>>> How to:<br>
>>> <a href="https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api" rel="noreferrer" target="_blank">
https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api</a><br>
>>> Ensure you get the DCCID/CandID assigned by LORIS.<br>
>>><br>
>>> Then as a second step:<br>
>>> b. Use the imaging insertion pipeline<br>
>>> <<a href="https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets" rel="noreferrer" target="_blank">https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets</a>><br>
>>> to load your DICOMs.<br>
>>> You will want to first ensure that the PatientName header in the DICOMs<br>
>>> as well as tar package are correctly labelled with PSCID_DCCID_VisitLabel<br>
>>><br>
>>> -- Method 2: for BIDS-format datasets:<br>
>>> How to :<br>
>>> <a href="https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets" rel="noreferrer" target="_blank">
https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets</a><br>
>>><br>
>>> Be sure to use the *-c* and *-s* options when running the bids_import script,<br>
>>> to automatically create your candidates and sessions.<br>
>>><br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> How do i delete a Study? And everytime do i have to create a new<br>
>>> candidate to get DCCID and a PSCID?<br>
>>><br>
>>> *First execution:*<br>
>>><br>
>>> (loris-mri-python) lorisadmin@loris-VirtualBox:/data/loris/bin/mri$ ./<br>
>>> <a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">
batch_uploads_imageuploader.pl</a> -profile prod < ~/Desktop/input.txt ><br>
>>> log.txt<br>
>>> Use of uninitialized value $_ in pattern match (m//) at ./<br>
>>> <a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">
batch_uploads_imageuploader.pl</a> line 144.<br>
>>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign<br>
>>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`<br>
>>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at<br>
>>> /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<br>
>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';<br>
>>> SET<br>
>>> @x1='242126',@x2='Achieva',@x3='3.2.2\3.2.2.0',@x4='34037',@x5='Philips<br>
>>> Medical Systems';<br>
>>> EXECUTE s USING @x1,@x2,@x3,@x4,@x5;<br>
>>> Error obtained:Cannot add or update a child row: a foreign key<br>
>>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1`<br>
>>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)<br>
>>><br>
>>> ERROR: The validation has failed. Either re-run the validation again<br>
>>> and fix the problem. Or re-run tarchiveLoader.pl using -force to force the<br>
>>> execution.<br>
>>><br>
>>><br>
>>> The tarchiveLoader.pl insertion script has failed.<br>
>>> Can't exec "mail": No such file or directory at ./<br>
>>> <a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">
batch_uploads_imageuploader.pl</a> line 249.<br>
>>> print() on closed filehandle MAIL at ./<a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">batch_uploads_imageuploader.pl</a><br>
>>> line 250.<br>
>>> print() on closed filehandle MAIL at ./<a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">batch_uploads_imageuploader.pl</a><br>
>>> line 251.<br>
>>><br>
>>><br>
>>> *And second execution: *<br>
>>><br>
>>> (loris-mri-python) lorisadmin@loris-VirtualBox:/data/loris/bin/mri$ ./<br>
>>> <a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">
batch_uploads_imageuploader.pl</a> -profile prod < ~/Desktop/input.txt ><br>
>>> log.txt<br>
>>> Use of uninitialized value $_ in pattern match (m//) at ./<br>
>>> <a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" 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<br>
>>> inserted:<br>
>>><br>
>>> * Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy<br>
>>> * Archive target location :<br>
>>> /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<br>
>>> ImagingUpload-18-33-Qq7HGy.tar<br>
>>> * md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec<br>
>>> ImagingUpload-18-33-Qq7HGy.tar.gz<br>
>>> * md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053<br>
>>> 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 ./<br>
>>> <a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">
batch_uploads_imageuploader.pl</a> line 249.<br>
>>> print() on closed filehandle MAIL at ./<a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">batch_uploads_imageuploader.pl</a><br>
>>> line 250.<br>
>>> print() on closed filehandle MAIL at ./<a href="http://batch_uploads_imageuploader.pl" rel="noreferrer" target="_blank">batch_uploads_imageuploader.pl</a><br>
>>> line 251.<br>
>>><br>
>>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> Ok, this sounds like good progress. Let us know when you next encounter<br>
>>> issues as you progress through the Imaging Install/Setup docs<br>
>>> <<a href="https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md" rel="noreferrer" target="_blank">https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md</a>>.<br>
>>> I'll look into how we can better handle the incoming/ directory next<br>
>>> time.<br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is<br>
>>> populated correctly except its port is 'port' : ''. Also i have tested<br>
>>> that i can connect to MySQL with lorisuser.<br>
>>><br>
>>> I executed the script again, because the only error i had previously was<br>
>>> that the /data/incoming folder didn't exist and there are no errors<br>
>>> reported back except of warnings <<mysql: [Warning] Using a password on the<br>
>>> command line interface can be insecure>>.<br>
>>><br>
>>><br>
>>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> It's possible -- if the script was unable to connect to the database<br>
>>> during its execution (e.g. typo in the password), that would explain the<br>
>>> underpopulated Image path and Loris-MRI code path you saw in the Config<br>
>>> module.<br>
>>> It's hard to tell without seeing the output from your script run -- Did<br>
>>> you see a sign of any such error?<br>
>>> The Config fields are populated by the imaging_install.sh script (starting<br>
>>> at line 222<br>
>>> <<a href="https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222" rel="noreferrer" target="_blank">https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222</a>><br>
>>> )<br>
>>><br>
>>> For example, check if the database connection information was populated<br>
>>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py<br>
>>><br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>><br>
>>><br>
>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi Christine,<br>
>>><br>
>>> If you are referring to the imaging_install.sh here is an image with the<br>
>>> configurations i typed. Maybe the problem is somewhere at the last part<br>
>>> which asks to configure as much as possible automatically?<br>
>>><br>
>>> Thanks<br>
>>><br>
>>><br>
>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. <<br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a>> ??????:<br>
>>><br>
>>> Hi Sotirios,<br>
>>><br>
>>> Glad to hear your LORIS core install is up and working and all the<br>
>>> front-end pages are loading.<br>
>>><br>
>>> > lorisadmin@loris-VirtualBox:/var/www/loris$ chmod 775 project<br>
>>> > and the web interface worked.<br>
>>><br>
>>> Yes, it's important that project/ have 775 permissions and that<br>
>>> lorisadmin be part of the sudoers group, per step 1 in the install<br>
>>> Readme <<a href="https://github.com/aces/Loris#install-steps" rel="noreferrer" target="_blank">https://github.com/aces/Loris#install-steps</a>>.<br>
>>><br>
>>> > As for the Paths, LORIS-MRI code and Image should change LORIS to<br>
>>> loris, right?<br>
>>><br>
>>> These imaging paths will be updated during your imaging installation<br>
>>> <<a href="https://github.com/aces/Loris/wiki/Setup" rel="noreferrer" target="_blank">https://github.com/aces/Loris/wiki/Setup</a>> by an automated script --<br>
>>> you do not need to set them manually via the Config module.<br>
>>> Please continue to follow the Setup Guide<br>
>>> <<a href="https://github.com/aces/Loris/wiki/Setup" rel="noreferrer" target="_blank">https://github.com/aces/Loris/wiki/Setup</a>> for detailed steps to follow.<br>
>>><br>
>>> Best,<br>
>>> Christine<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> wrote:<br>
>>><br>
>>> As for the Paths, LORIS-MRI code and Image should change LORIS to loris,<br>
>>> right?<br>
>>><br>
>>> [image: image.png]<br>
>>><br>
>>><br>
>>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos <<br>
>>> <a href="mailto:sotirisnik@gmail.com" target="_blank">sotirisnik@gmail.com</a>> ??????:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> i used<br>
>>><br>
>>> curl -sL <a href="https://deb.nodesource.com/setup_8.x" rel="noreferrer" target="_blank">
https://deb.nodesource.com/setup_8.x</a> | sudo -E bash -<br>
>>> sudo apt-get install -y nodejs<br>
>>><br>
>>><br>
>>> you had suggested in the past, make worked and now i can see all the<br>
>>> contents in the web-interface, but i don't need make install?<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>><br>
>>> <a href="mailto:christine.rogers@mcgill.ca" target="_blank">christine.rogers@mcgill.ca</a><br>
>>> McGill Centre for Integrative Neuroscience | MCIN.ca<br>
>>> Montreal Neurological Institute<br>
>>> McGill University | Montreal | Canada<br>
>>><br>
>>> _______________________________________________<br>
>>> Loris-dev mailing list<br>
>>> <a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
>>> <a href="https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev" rel="noreferrer" target="_blank">
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a><br>
>>><br>
>>><br>
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<br>
End of Loris-dev Digest, Vol 64, Issue 16<br>
*****************************************<br>
</blockquote>
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</blockquote>
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<a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
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</blockquote>
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<div><br>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote></div>
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<a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
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</blockquote></div>