<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">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 class="gmail_quote"><div dir="ltr" class="gmail_attr">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 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 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 class="gmail_quote"><div dir="ltr" class="gmail_attr">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 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>
<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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 class="gmail_quote" 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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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 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 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" id="gmail-m_-3167548388594440731gmail-m_3548729294308866586gmail-m_-7226580865415254747gmail-m_792347981290930428gmail-m_-8197080047898918979gmail-docs-internal-guid-3d4118f8-7fff-7020-bc97-01217b928349"><span style="border:medium none;display:inline-block;overflow:hidden;width:643px;height:237px"><img src="https://lh5.googleusercontent.com/0G4f5Ms034ZaYEwHLLOzo4YBjQwcKxjSLRrE0XLZAR86JhsPocXi5tkAvgbELadS63HWgJ_A6eGF0BitFWhf4DCVx5EEFzThQm19QfKDpgrrIfGFZjdy4BanrmRjawJeo3kYt-5y" style="margin-left: 0px; margin-top: 0px;" width="643" height="237"></span></span></div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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 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 src="cid:16d18ad27abcb971f169" alt="image.png" width="568" height="121"></div>
<div><br>
</div>
<div>
<div><br>
</div>
<div><img src="cid:16d18ad27abcb971f16a" alt="image.png" width="549" height="568"></div>
<div><br>
</div>
<div>Thanks<br>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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 see that i can edit the values but not how to insert new rows.<br>
</div>
<div><br>
</div>
<div><img src="cid:16d18ad27abcb971f167" 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 src="cid:16d18ad27abcb971f168" alt="image.png" width="284" height="262"><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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 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 src="cid:16d18ad27abcb971f166" alt="image.png" width="533" height="27"><br>
</div>
</div>
<div>
<div><br>
</div>
<div>
<div><img src="cid:16d18ad27abcb971f165" 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 src="cid:16d18ad27aacb971f164" 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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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> Here is the psc table<br>
</div>
<div><img src="cid:16d18ad27aacb971f162" 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 src="cid:16d18ad27aacb971f163" 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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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">
<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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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">
<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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>/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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>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 class="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_-8226803066969393218m_-3978559249485041190gmail-pl-smi" 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 class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>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 style="border:medium none;display:inline-block;overflow:hidden;width:643px;height:345px" id="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"><img src="https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs" style="margin-left: 0px; margin-top: 0px;" width="643" height="345"></span></div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>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 class="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-m_-4480004644065686266gmail-Apple-interchange-newline">
</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>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">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 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>As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right?<br>
</div>
<div><br>
</div>
<div><img src="cid:16d18ad27aacb971f161" alt="image.png" width="474" height="332"></div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">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>
</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 used</div>
<div><br>
</div>
<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 class="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-m_-4480004644065686266gmail-m_6037970262854185989gmail-m_1088120395401920242gmail-il">nodejs<br><br></span></code></pre>
</div>
<div><br>
</div>
<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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<div dir="ltr" class="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-m_-4480004644065686266gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<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>
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<div><br>
</div>
-- <br>
<div dir="ltr" class="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_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<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>
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