[Loris-dev] Questions and errors uploading BIDS
Cecile Madjar
cecile.madjar at mcin.ca
Mon Jul 19 15:35:05 EDT 2021
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> 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> wrote:
>
> External Email - Use Caution
>
> 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
>>>
>>>
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>>
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>
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