[Loris-dev] MINC insertion
Morales Pinzon, Alfredo
AMORALESPINZON at BWH.HARVARD.EDU
Fri Dec 10 14:12:12 EST 2021
Hi Cécile,
We managed to import some MINC files with the proper thumbnails in LORIS. The files seem to be properly stored in the hard drive but we are facing the following issues:
1. When loading them in the front-end the MINC images cannot be visualized
2. When getting the headers usign the API we are getting {"error":"not found"}
3. When downloading them using the API we get the error code "404"
Any ideas?
On a side note, how can I change the acquistion label of an acquisition that I uploaded with an improper label?
Thank you for your help.
Best,
Alfredo.
On Nov 30, 2021, at 11:19 PM, Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.EDU>> wrote:
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Hi Cécile,
Thank you. 4pm works. I’ll send a send in a separate email.
Best,
Alfredo.
Get Outlook for iOS<https://secure-web.cisco.com/1PNz5U6EhZ9bpIT12Ja8UKYftUkpn_Raq5yJAq5UlUVrzASfWdBGB_NTKH4r4SdXViI-uWyNsITpiECc6lxGRXh1u3HE4UmK6DiIO4pPwbV1b24od2Cv8ptLxRGkuzK6CSy10s58NjPqm5Ffi1QeTzQouRc_9aAMW3D-5patrAXX3y0Hjmx8e_SoiiVUKcweg2W7TnPI0rqDenpUUoAsZPjYbr5o3UUykL385AC-_2dv9lxhFXEgV6pey6erqBaWmS3sbqwA3-jsSkIjQDLK5nUtz1EeRnH3NsrT4jFbU5iCV2LtY8B8G19ot6upbSxA7oBDZbHJQ6XX_V2LtFjJlvw/https%3A%2F%2Faka.ms%2Fo0ukef>
________________________________
From: Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>>
Sent: Tuesday, November 30, 2021 4:15:28 PM
To: Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.EDU>>
Cc: 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>>; Sridar Narayanan <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>>; Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca<mailto:rozie.arnaoutelis at mcgill.ca>>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca<mailto:douglas.arnold at mcgill.ca>>; Guttmann, Charles,M.D. <guttmann at bwh.harvard.edu<mailto:guttmann at bwh.harvard.edu>>; Istvan Akos Imre Morocz, Dr <istvan.morocz at mcgill.ca<mailto:istvan.morocz at mcgill.ca>>; Samir Das <samirdas99 at gmail.com<mailto:samirdas99 at gmail.com>>
Subject: Re: [Loris-dev] MINC insertion
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Hi Alfredo,
Sorry for the delay. Time flies quickly this week.
How about a Zoom call tomorrow (Wednesday) at 10:30AM or at 4PM?
Let me know if one of those times works for you.
Thanks!
Cécile
On Mon, Nov 29, 2021 at 1:30 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cécile,
Here is the results of the query:
===
mysql> SELECT * FROM psc WHERE CenterID=843 \G;
*************************** 1. row ***************************
CenterID: 843
Name: inf_0102
PSCArea: NULL
Address: NULL
City: NULL
StateID: NULL
ZIP: NULL
Phone1: NULL
Phone2: NULL
Contact1: NULL
Contact2: NULL
Alias: BGI
MRI_alias: BGI
Account: NULL
Study_site: Y
1 row in set (0.00 sec)
===
Alias and MRI_alias look fine. What should we look into now? We can debug over Zoom if that works for you.
Best,
Alfredo.
On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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Hi Alfredo,
I think we are indeed narrowing where the error happens. It looks like for some reason this getPSC<https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm> function is returning "UNKN", 0. It might be related to the Alias or MRI_alias content of the psc table for CenterID 843.
What do you get when you run the following query?
SELECT * FROM psc WHERE CenterID=843;
In the Alias or MRI_alias column, you should be able to see BGI so that the scanner candidate can be identified with the proper site.
Let me know,
Cécile
On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cécile,
Thank you, it looks like we’re getting closer to find a solution. Find the answers to your questions inline below.
Happy to debug over Zoom if it’s easier for you.
Best,
Alfredo.
On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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Hi Alfredo,
I notice that the CenterID for the site is 0. Do you have an entry in the psc table for a CenterID=0?
No, we don’t have it. The CenterID starts at 1.
===
select * from psc where CenterID=0;
Empty set (0.00 sec)
===
The problem here is that the data comes from a new scanner and the pipeline tries to first register a new candidate for the scanner (scanner candidate) before adding an entry in the mri_scanner table. To determine the site of the scanner, the pipeline uses the determinePSC<https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503> function of MRIProcessingUtility.pm (called by minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> in line 454<https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>). I would be curious to see what the $center_name and $centerID values returned are.
These are the returned values. Maybe we need to look deeper into this.
===
determinePSC->Center name: UNKN
determinePSC->Center ID: 0
===
Could you also copy the code you have in your prod file for the function getSubjectIDs?
You mean this file “mri/dicom-archive/.loris_mri/prod”, right? Find the function enclosed.
Finally, could you check that the candidate BGI102001_207019 does have a RegistrationCenterID set and if there is already a screening session created in the session table, that the CenterID of that session has properly been set?
The candidate has a RegistrationCenterID (843):
===
select * from candidate where CandID=207019 \G;
*************************** 1. row ***************************
ID: 8974
CandID: 207019
PSCID: BGI102001
ExternalID: NULL
DoB: 1969-05-15
EDC: NULL
Sex: Female
RegistrationCenterID: 843
RegistrationProjectID: 12
Ethnicity: NULL
Active: Y
Date_active: 2021-05-27
RegisteredBy: dataman
UserID: dataman
Date_registered: 2021-05-27
flagged_caveatemptor: false
flagged_reason: NULL
flagged_other: NULL
flagged_other_status: NULL
Testdate: 2021-06-09 10:55:35
Entity_type: Human
ProbandSex: NULL
ProbandDoB: NULL
DoD: NULL
1 row in set (0.00 sec)
===
The session with the proper values already exists:
===
mysql> select * from session where CandID=207019 and Visit_label="screening" \G;
*************************** 1. row ***************************
ID: 127260
CandID: 207019
CenterID: 843
VisitNo: 1
Visit_label: screening
SubprojectID: 2
Submitted: N
Current_stage: Not Started
Date_stage_change: NULL
Screening: NULL
Date_screening: NULL
Visit: NULL
Date_visit: NULL
Approval: NULL
Date_approval: NULL
Active: Y
Date_active: 2021-05-27
RegisteredBy: dataman
UserID: dataman
Date_registered: 2021-05-27
Testdate: 2021-06-10 18:35:41
Hardcopy_request: -
BVLQCStatus: NULL
BVLQCType: NULL
BVLQCExclusion: NULL
QCd: NULL
Scan_done: Y
MRIQCStatus:
MRIQCPending: N
MRIQCFirstChangeTime: NULL
MRIQCLastChangeTime: NULL
MRICaveat: false
ProjectID: 12
languageID: 1
1 row in set (0.00 sec)
===
Thank you!
Cécile
On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cécile,
Thank you for answer.
I included the following lines:
===
. " NOW(), 'NeuroDB::MRI', 'Scanner' ) ";
+ print "\nCenter ID: " . $centerID . "\n\n";
+ print "\nQuery:" . $query . "\n\n";
$dbh->do($query);
}
===
And I got the following output:
===
perl minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics
log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? )
Center ID: 0
Query:INSERT INTO candidate (CandID, PSCID, RegistrationCenterID, Date_active, Date_registered, UserID, Entity_type ) VALUES (442627, 'scanner', 0, NOW(), NOW(), 'NeuroDB::MRI', 'Scanner' )
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1020.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
SET @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===
I think it’s important to mention that this candidate was created by the bids importing script. Maybe there is center associated with the candidates when using the bids script?
Let me know your thoughts.
Best,
Alfredo.
On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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Thank you Alfredo.
I wonder whether the variable $centerID is null when provided to the query here<https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012> in your case.
Could you add in MRI.pm line 1018 the following print statements and let me know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);
Thank you!
Cécile
On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cécile,
This is the branch that we are using in the IPMSA project:
https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA<https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>
Best,
Alfredo.
On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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Hi Alfredo,
Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.
Thank you!
Cécile
On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cécile,
I’m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:
===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===
Could you help me figuring out what is happening? Is there something I should add to the minc headers?
Best,
Alfredo.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/14m8jq3YFX-kL4WHSOD3NyklDH3_1jO6LrSN9gvfM5CyvUtE7cihaLOo51ulZdVQKgs5rOFUrgJxphRC2W3gjEcYsYyqJP3GlMV3sJHwLGLwsGvslUlp9df_5QkEDbk0OiO4v-SgA4uMhT6od0larJxEIegxbPKpy9GmlloLw6cDlPw0voUhi7Y0kxA_zjwDvxaVMhZ7RIpojsrcwl2crdOHamo_wQI9pz9cAU_qxwUGkhiSfwtcCe8i-UtBjbSEY9dM0SpejAYJqhqEpOK_aCqQ4_wOl8FxQWWNK2nOsD7QawkuH5liIxDIL5XojDqICa2oljEN17RtZIEy425vItA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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