[Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id

Tue Nov 22 11:35:24 EST 2022

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>
Date: Thu, Nov 17, 2022 at 10:24 AM
Subject: Re: [Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
To: loris-dev at bic.mni.mcgill.ca <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 -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 (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 -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' <loris-dev at bic.mni.mcgill.ca>
*Asunto:* 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 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 -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 [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 -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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