[Loris-dev] Questions and errors uploading BIDS
Morales Pinzon, Alfredo
AMORALESPINZON at BWH.HARVARD.EDU
Fri Jul 23 10:57:55 EDT 2021
Hi Cécile,
I changed the Current_stage to Not Started for the visits that had it in NULL. Now I can see all the visits in the front-end. Thank you!
Regarding the scan_acquisition_time, would it be possible to debug it over a Zoom call. As I mentioned I have in place the file *_scans.tsv but the acquisition date is not in the database after insertion.
Best,
Alfredo.
On Jul 19, 2021, at 3:35 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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You can change the Current_stage to Not Started for those two visits then.
It should not be affecting the scan_acquisition_time since that information is stored in parameter_file and not the session table.
Hope this helps,
Cécile
On Mon, Jul 19, 2021 at 3:07 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cécile,
Yes, I think two out of three visits had Current_stage NULL, what should value should it be? Is it enough to change it from NULL to “something_else”?
Does this impact the scan_acquisition_time?
Best,
Alfredo.
On Jul 19, 2021, at 1:41 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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Hi Alfredo,
The issue here is that the first session has a Current_stage set as NULL. Maybe verify which session has Current_stage set to NULL. Maybe it comes from an old import?
On Mon, Jul 19, 2021 at 11:41 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cécile,
Thank you for the prompt reply. Here are the results for the queries:
===
SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;
Empty set (0.00 sec)
===
===
SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;
+---------------+
| Current_stage |
+---------------+
| NULL |
| Not Started |
+---------------+
2 rows in set (0.01 sec)
===
As I said before, we can have a call if this makes things easier and faster.
Best,
Alfredo.
On Jul 19, 2021, at 11:26 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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Hi Alfredo,
For the acquisition date, try the following query:
SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;
For 2., what does the following query return?
SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;
Cécile
On Mon, Jul 19, 2021 at 11:19 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cécile,
I patched LORIS and inserted one visit.
Before moving forward I want to make sure the acquisition date was inserted, could you please tell me what is the “ParameterFileID” for the acquisition date, I looked at the table parameter_file using one of the FileIDs from the last insertion but couldn't find the acquisition date. See the result of the query below.
2. The front-end is still crashing. This is the log:
===
[php7:error] [pid 32588] [client 155.33.137.12:23564<http://secure-web.cisco.com/1nROtbNw-Vzt6PDAU71bMpkZ2DX-C8_gGT7jPalLUwf7iW0vRUudY_S6vIhtCPN4YHMDNIlD9L_XfAEixBt2iRg_KHw6treMqgGID9xjB3xoxlLD2fhNblD3jlfGfUSZYqaMb2TZKSCJoVCGMoDx12cEmnzWRfPe2QxGRgwYHNP7Bf9SBcfWaAQ_ODCTQVBimXbr1NWavp5WNDM_hcGsLLupgF6xBbXBxr7s1e7BLCemInf4-AlIdok-y3-ZvC8BDdDbKsCs7sHYqn0gSK7YQsA/http%3A%2F%2F155.33.137.12%3A23564>] PHP Fatal error: Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www/loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageDecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.inc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1mVIQ6ONSXAF7-5MPbIxuWHNbxYUn-M6MiKm-VfZKDScn_0YJ02NPcV4p7rirYg2XnVfXdHzODTPAcrLuUItZ6KKzzEdJ2lQXp9ZTMufpswd6YsZlGwob5GriUoRzGl7WJKfUwk2hnizx5FQXgIT0jZjFQqSf0w-2sproV85wbmg5r4X4UtFMV9WCoOG__khDbsnWOcdGaPJHTS1tVcjVuS2tRv628XtslAP_5jnzzfTPMndhvwR3-tRMLUp_ptV7i_ww353-P3KHxecwTBVnXg/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
===
Happy to have a Zoom call if it helps.
Thank you for your help.
Best,
Alfredo.
===
select ParameterFileID,Value from parameter_file where FileID=428983;
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
| ParameterFileID | Value |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
| 109949932 | MR |
| 109949967 | 130 |
| 109949981 | 0.9765625 |
| 109949977 | syngo_MR_A35_4VA35A |
| 109949958 | 12:13:34.360020 |
| 109949968 | t1_RIPOSIZ. |
| 109949973 | SK_SP_OSP |
| 109949962 | 2D |
| 109949960 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189] |
| 109949982 | 0.9765625 |
| 109949975 | 5 |
| 109949969 | CP_HeadArray |
| 109949965 | 70.3125 |
| 109949966 | i |
| 109949945 | 0.187383 |
| 109949978 | 3 |
| 109949963 | 1.5 |
| 109949976 | 3 |
| 109949970 | 0.655 |
| 109949964 | HFS |
| 109949974 | t1_RIPOSIZ. |
| 109949971 | SE |
| 109949956 | 99 |
| 109949959 | 0.01 |
| 109949930 | Siemens |
| 109949957 | 1 |
| 109949983 | 2.9999998 |
| 109949985 | 207019/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w_ZZZ_check.png |
| 109949972 | _tse2d1_5 |
| 109949914 | 20140629 |
| 109949915 | 99 |
| 109949916 | 1 |
| 109949917 | 12:13:34.360020 |
| 109949918 | 256 |
| 109949919 | dcm2niix |
| 109949920 | v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC7.3.0 |
| 109949921 | 0.01 |
| 109949923 | 150 |
| 109949924 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189] |
| 109949925 | ['ORIGINAL', 'PRIMARY', 'M', 'ND'] |
| 109949926 | ROW |
| 109949928 | 2D |
| 109949929 | 1.5 |
| 109949931 | Sonata |
| 109949933 | 1 |
| 109949934 | HFS |
| 109949935 | 70.3125 |
| 109949936 | i |
| 109949937 | 100 |
| 109949938 | 0.55 |
| 109949939 | 130 |
| 109949940 | t1_RIPOSIZ. |
| 109949941 | %SiemensSeq%_tse |
| 109949942 | CP_HeadArray |
| 109949943 | 512 |
| 109949944 | 0.655 |
| 109949946 | SE |
| 109949947 | _tse2d1_5 |
| 109949948 | SK_SP_OSP |
| 109949949 | t1_RIPOSIZ. |
| 109949950 | 5 |
| 109949951 | [48, 57, 59, 361, 234, 67, -246, 256] |
| 109949952 | 3 |
| 109949953 | syngo_MR_A35_4VA35A |
| 109949954 | 3 |
| 109949955 | 202.922 |
| 109949961 | ['ORIGINAL', 'PRIMARY', 'M', 'ND'] |
| 109949979 | bids_imports/INFORMS_BIDSVersion_1.4.0/sub-ANOM/ses-endoftreatment/anat/sub-ANOM_ses-endoftreatment_run-1_T1w.json |
| 109949980 | 7655f29d97c14a6b88055f99c7879097650c31cafa7405a1ad3a93062d04669417f42b67c175e9ad904da1e1bb677b2fb6a44ed8b26af482a4d3c40498f284df |
| 109949984 | 3f487183fe830d801477568aec824c967a44d3bf3feb9cbd6575830d31b90b089cc625a037c487d3985fb10ee0a00f2eac824980955949c8955cdd304ea838b9 |
| 109949922 | 5 |
| 109949927 | 1 |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
===
This is the content of the *_scan.tsv file:
===
filename acq_time
anat/sub-ANOM_ses-endoftreatment_run-1_T1w.nii.gz 2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w.nii.gz 2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_FLAIR.nii.gz 2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-2_T1w.nii.gz 2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_PD.nii.gz 2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_T2w.nii.gz 2014-06-29T00:00:00
===
On Jul 15, 2021, at 5:23 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
External Email - Use Caution
Hi Alfredo,
Sorry for the delay, I had to take a deeper look at the code to answer some of your questions. See below.
> 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in the BIDS standard (https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file<https://secure-web.cisco.com/1RT0b_pDRzGh5oEnKt7wHclfIWMewUlzzoH-FStRocNdjI2mrpqsgr33eVaIS22zsvLSZ7Z8ugyaoZ07SHA_O7tObAB409DokII49oyHlFVQnGqaaxEoC_87rcI6ivzH41s36uv9R13FRzaiRJPDhbqmj3kt67BF36UEJp4e5xglyAHPcxx1DV8sf3sJ2TRBCKhNhHUWeRbPM9DdNrFxpoZzYHnN4xy-VMBRK5T9SF4afE6jv3tqdaKdfSYG2wDh-CWrIBbzyeSECIRnMYikelA/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23scans-file>) to add the acquisition dates, do you take it into account to set the dates in LORIS? If not, how can I set the acquisition dates for the images in the session/visit?
Indeed, if you enter a date under an 'acq_time' column in the scans.tsv file, it will add an entry in parameter_file for the scan_acquisition_time parameter.
>
> 2. I am doing the insertion visit by visit to be able to identify issues instead of running all the subjects at once. In this approach I get an error stating that the participants file (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is different from for every execution. Is there a way I can upload subject by subject without having this issue?
yeah, this is a current limitation that this file keeps changing each time you upload a new candidate. The pipeline was initially developed for retrospective BIDS datasets. We would need to modify this part<https://secure-web.cisco.com/1FA74HdTiHzhrcJezSt2K6DKMGwP_wqxcdk1oXclu1U6jCz4rd2fSi-NwskWq_Qfb0p4MTUX6_XEbTFvgo_VxzSI4YiWtniz3W9Yi_Y_Yhd3GKBQD7kKnXK8l0jqEWj-6sZ77YTpIg9X5O235SfFeZ3JW3V5MFXQOH7vMnzgPDBS-6dsjvmCAtnAjP4DJoXkGwQ6VJLV21yWj9np6NfjWvjphVgXfpYnIoS4jb57yVl8xBW0ttGeejb-HEHsaZ-bNfre-16KCLmR-IJO3pZbnwg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fb5a6fc8cc3cf1fad50df21d9d87a284981705e3c%2Fpython%2Fbids_import.py%23L299> for prospective datasets so that instead of just trying to copy the participants.tsv file, if it already exists, it would append a row into the already existing file. You can find a fix for that in the following PR https://github.com/aces/Loris-MRI/pull/645<https://secure-web.cisco.com/1Tpg7v8DtF0HJJEnPZUNGN7gwCdF7vLrM19WZmYU8p4-riYcbJ1FVNYH0FGEvIBT0KwSYUMgtVeulxeEaGSohphmm0NQn8wIbxh5cSX4VwbKcKLhvQY1RtnS2SxEKUi4Pln5KHxRYDcVhz9sWnZ6EIhfZEDECvkuT2-zTt24B5MMeBduiQG8W3Pqa7Qr2oEjJW_m84bq0EVtbGQmu5ZVKytj8tPkwWAUE8gTEtLOb1DjwDX5O8y8EHAN_8lf2ZqJ9eojMRDufJj2QObf0g02n3Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F645>.
>
> If l have to launch the whole dataset, is the bids script able to check what was already inserted in case there is an error and I have to it again?
Yes, the pipeline is supposed to be smart enough to not reinsert something that was previously inserted.
>
> 3. After insertion of BIDS for a subject in a visit I cannot access the visit in the front end, I am getting a 500 error. Here is the error log in LORIS:
>
> ===
> [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client 216.15.126.108:55424<http://secure-web.cisco.com/1WYhYdfRTqaTteJ_4rndbHmww7uTfLympsocUwkjHV2oHQVOQ_ddIjv7AcfCoiP5cJIbw5iksCEFI9RVOxA3_lM6etO-PCaDz89PgNjaEjQPMC5dEfLOft3B7YhP7TCF4ISn-hvCOCFnhQqmRbs9zS1PRbVr6qe_Fra0AR2dZzskzHnYp2A_u29fTzE5u8vYJLMpl4t10wah4Bga-hhoD3gkgnRHVU5KAWy4uwX30Ma4tng8DnVlqBopiM9DpYE6ZEviZpdmHvWqJZxPHxbnHOw/http%3A%2F%2F216.15.126.108%3A55424>] PHP Fatal error: Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www
> /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(
> 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageD
> ecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.i
> nc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
> 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1XkKe3e3JkFCEbEAQx3rrZ25ZCaDXFH7ViiHfRCVtt0ZTI9ckG_4i5CYOnY_Wv0SYfmdvUUZ0jQkdjvUgzKY9qJfqnqcVF_7n2nRaR-c1a4U_Y95LN-Dv96I8j-OBHltZ52DoTaYZ9RvB7YL9vP82yG9pUb2XlYJwK6xA6b2gGwhHhyqpdrPfRW0HZFx4__6pDI4CU5CQWx9_dteaDW3_xjntBo3296km9H-nJNiywrGrKtv_1pO6wCU5ygXs2bqXwZ9j7X4eILwCv0N7S7PlKA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
> ===
This might be due to the Current_stage not being set when creating the visit via the bids_import.py script. Here is a PR to fix that issue next time you import a new visit via bids_import.py: https://github.com/aces/Loris-MRI/pull/644<https://secure-web.cisco.com/1RuRCEtVgtWrK7Pm95g10P8zRltmw5fqwt4wM4vzTM2N7zp7p8HXJKNSQo5QSAfOa23ID04z8m13DojdlnneipDRp6yoYNUJIoorexU5ixp49Alwi5aaHokrOmz-gRnpRkrUxMNI04i2tsCDBAsyiwIBoMwgWyCGHg8asEvLiHrEcYtWAdRycS4UQ7Udt6hrVhp6DqF6kpBH3s4oWPPlFvnJ9CHywNOno0NqHI0zXVnlWI2BuIW0heLJeaDSyrvK-5FcYxqhfnBEJTq1hkNB-Jg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F644>
Hope this helps,
Cécile
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