[Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
Cecile Madjar
cecile.madjar at mcin.ca
Wed Nov 23 09:11:12 EST 2022
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> 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>
> *Enviado el:* martes, 22 de noviembre de 2022 17:35
> *Para:* Olano.María <molano at ext.cnio.es>; loris-dev <
> loris-dev at bic.mni.mcgill.ca>
> *Asunto:* 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>
> 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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> destinatario. Se prohíbe la distribución, reproducción o cualquier otro
> tipo de transmisión por parte de otra persona que no sea el destinatario.
> Si usted recibe por error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protección de los datos personales de las personas físicas, la
> información personal que nos pueda facilitar a través de este correo
> electrónico quedará registrada por la Fundación CNIO con la finalidad de
> tramitar el objeto del presente correo electrónico. El tratamiento de sus
> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no serán comunicados
> a ningún destinatario salvo a aquellos que usted nos autorice o así venga
> exigido por una ley. Ud. podrá ejercer los derechos de acceso,
> rectificación, supresión, limitación de tratamiento, portabilidad y
> oposición en la siguiente dirección: c/Melchor Fernandez Almagro 3, 28029
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> información adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha información adicional en el siguiente enlace dentro de
> nuestra página web: https://www.cnio.es/es/privacidad/index.asp
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> **LEGAL NOTICE**: This email and any attached files may contain protected
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> Pursuant to the provisions of EU Regulation 2016/679 regarding the
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