[Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
Olano.María
molano at ext.cnio.es
Wed Nov 23 09:39:23 EST 2022
Hi Cecile,
Can’t thank you enough, that was exactly what we needed for it to work!
De: Cecile Madjar <cecile.madjar at mcin.ca>
Enviado el: miércoles, 23 de noviembre de 2022 15:11
Para: Olano.María <molano at ext.cnio.es>
CC: loris-dev <loris-dev at bic.mni.mcgill.ca>
Asunto: Re: imaging_non_minc_insertion.pl issue with scanner_id
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe
Hi Maria,
It looks like the following SQL patch has not been run to update the MRI tables. Try sourcing this upgrade patch<https://github.com/aces/Loris/blob/v24.1.1/SQL/Release_patches/24.0_To_24.1_upgrade.sql> and the script should work.
Let me know how it goes,
Cécile
On Wed, Nov 23, 2022 at 6:53 AM Olano.María <molano at ext.cnio.es<mailto:molano at ext.cnio.es>> wrote:
Hello Cecile!
Thank you for your kind response. You were completely correct, the problem was the visit label not being read correctly, but we managed to solve this by adding an optional parameter: patient_name as seen below
(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> -profile prod -upload_id 1 -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose -patient_name DCC0000_359572_V3
However, this proved to come with its fair share of errors, it seems the file Is read well and moved to another location (/data/loris/data/assembly/359572/V3/mri/native/) but the console output reads as follows:
log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-12-20-gEsQPj.log.
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3
-> ScannerID was set to 1
-> SessionID was set to 1
-> Acquisition date was set to 2012-04-20
-> Output type was set to native
Acquisition date: 2012-04-20
DBD::mysql::db do failed: Unknown column 'PhaseEncodingDirection' in 'field list' at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 793.
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 818.
We had the idea of adding another parameter indicating there was a json file with said Phase encoding direction inside ((loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> -profile prod -upload_id 1 -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose -patient_name DCC0000_359572_V3 -metadata_file /home/lorisadmin/Downloads/patient.json) , but it was of no use, the console sent us the same message.
Inside the log file FileLoad-12-20-gEsQPj.log here is what is written:
==> computing md5 hash for MINC body.
--> md5: aab815082fbf91e7e3e26b7f6b899e2d
File /home/lorisadmin/Downloads/DCC0000_359572_V3.zip
moved to:
/data/loris/data/assembly/359572/V3/mri/native/loris_359572_V3_t1_001.zip
ative
And the MRICandidateErrors has an empty set.
Any help would be much appreciated, best regards!
María
De: Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>>
Enviado el: martes, 22 de noviembre de 2022 17:35
Para: Olano.María <molano at ext.cnio.es<mailto:molano at ext.cnio.es>>; loris-dev <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>
Asunto: imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> issue with scanner_id
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe
Dear Maria,
Sorry for the late reply. For some reason I never received your email. Luckily, someone else from the LORIS team just flagged it and sent it to me.
It looks like the latest issue you are encountering is that the visit label is not properly parsed by the getSubjectIDs function in your prod file. Instead of returning V3, it returns V3.zip which is most likely not a valid visit label for your project.
The other possibility could be that DCC0000 and 359572 do not refer to the same candidate.
In any case, I think for both situations, an entry has been added to the MRICandidateErrors table and you could see the file in the MRI violations module where the file would be logged there.
Let me know if that helps. Best,
Cécile
---------- Forwarded message ---------
From: Olano.María <molano at ext.cnio.es<mailto:molano at ext.cnio.es>>
Date: Thu, Nov 17, 2022 at 10:24 AM
Subject: Re: [Loris-dev] imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> issue with scanner_id
To: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>
Good afternoon!
We managed to solve the issue with the scanner_id by linking the CandID to the scanner
mysql> SELECT * FROM `mri_scanner`;
+----+--------------+---------+---------------+----------+--------+
| ID | Manufacturer | Model | Serial_number | Software | CandID |
+----+--------------+---------+---------------+----------+--------+
| 0 | NULL | NULL | NULL | NULL | NULL |
| 1 | SIEMENS | TrioTim | 35008 | Python | 359572 |
| 10 | NULL | NULL | NULL | NULL | NULL |
+----+--------------+---------+---------------+----------+--------+
And later got the upload_id error:
(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose
log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-11-48-F5qW5R.log.
ERROR: Invalid UploadID 1.
Managed to side step this error by using the front end Imaging Uploader which filled out the mri_upload table with the UploadID 1
mysql> SELECT * FROM `mri_upload`;
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
| UploadID | UploadedBy | UploadDate | UploadLocation | DecompressedLocation | InsertionComplete | Inserting | PatientName | number_of_mincInserted | number_of_mincCreated | TarchiveID | SessionID | IsCandidateInfoValidated | IsTarchiveValidated | IsPhantom |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
| 1 | lorisadmin | 2022-11-17 14:40:58 | /data/incoming/lorisadmin/DCC0000_359572_V3.zip | | 0 | NULL | DCC0000_359572_V3 | NULL | NULL | NULL | 1 | NULL | 0 | N |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
However! It didn’t manage to upload correctly so we tried to use the back end again with imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> (as this isn’t a DICOM file) and we are presented with our last error:
(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /data/incoming/lorisadmin/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose
log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-16-0-_g35H2.log.
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip
=> No Visit label
ERROR: Candidate IDs mismatch for /data/incoming/lorisadmin/DCC0000_359572_V3.zip.
This Visit label has been populated in the MySQL visit table, so we don’t know what mismatch it is referring to.
Any help would be much appreciated.
María
De: Olano.María
Enviado el: miércoles, 16 de noviembre de 2022 14:11
Para: 'loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>' <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>
Asunto: imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> issue with scanner_id
Good afternoon,
Hope this email finds you well. We are having problems using the imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> as when we execute the command this what pops up in the terminal.
(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 0 -coordin_space native -reckless -verbose
This script inserts a file in the files and parameter_file tables.
Usage: perl imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> [options]
-help for options
ERROR: missing -scanner_id argument
As you can see, scanner_id is included in the options accompanying the command, but when changing the ID from 0 to 10 it does recognize scanner_id, shown as followed:
(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 10 -coordin_space native -reckless -verbose
log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-12-49-8uubDY.log.
ERROR: Invalid ScannerID 10.
Both IDs are in the MYSQL table “mri_scanner” so we don’t know what the problem could be.
mysql> SELECT * FROM `mri_scanner`;
+----+--------------+-------+---------------+----------+--------+
| ID | Manufacturer | Model | Serial_number | Software | CandID |
+----+--------------+-------+---------------+----------+--------+
| 0 | NULL | NULL | NULL | NULL | NULL |
| 10 | NULL | NULL | NULL | NULL | NULL |
+----+--------------+-------+---------------+----------+--------+
Any help would be much appreciated.
Best regards,
María
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