[Loris-dev] Questions and errors uploading BIDS
Cecile Madjar
cecile.madjar at mcin.ca
Mon Jul 19 13:41:09 EDT 2021
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> 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> wrote:
>
> External Email - Use Caution
>
> 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> 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> 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
>>
>>
>> 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/12oS_QzclpiQcg_5CjSIubWkQntHnTzqFtBX6mIpa2UBfLh0PVFbNhw3IdXKR4AZ34z6Y4oONHxNl8RPg_-v5rbGH1bm25TzFr3nnHzzX-JiG9TdS5w_tGDS8dGTAdqHOqRD0y6Fn6ceB81q-IYVyZxyd-oWY8_bD4W7nK_hFDdMGi_GjLB5Qm-Opov0A6h0QkxNvnxJQpq85R1ace87QLIkJNTDBloRdcjKgYJm3NLT9JbBe-uOsotk5sBO21JKnuVHFKcIakn138zVhP4vF1A/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.
>>
>> Please note that this e-mail is not secure (encrypted). If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately. Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>
> 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.
>
> Please note that this e-mail is not secure (encrypted). If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately. Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20210719/2b8974e7/attachment-0001.html>
More information about the Loris-dev
mailing list