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MaximeBICMTLMaximeBICMTL
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physiological file download path
add raisinbread sql [SQL/MEG] Add the MEG CTF head shape tables (#10412) The MEG CTF format uses a `headshape.pos` file to register the head shape of the participant. This file is CTF-specific but BIDS-standard (the BIDS MEG specification basically allows to use native files of all specific data types), and is usually shared across all the MEG acquisitions of a session. This adds some tables to register this data in the LORIS physiological database and link it to the relevant MEG files. The `headshape.pos` file format is unfortunately very sparsely documented. It is a textual file format whose contents looks like this: ``` 85 1 5.60644227 -6.38055462 0.79194871 2 8.06310971 -4.72750212 0.59046631 3 7.58675759 -5.78050209 3.05185917 ... NAS 8.57169649 -0.14219376 -3.33998151 LPA -0.58286578 7.02263278 0.27529669 RPA -1.40471662 -7.10183109 0.57320080 ``` The first line is the number of points. The coordinates are in centimeters. It might be useful to use a proper `physiological_coord_system` in the future, but this can easily be added later IMO, so I'd like to start by merging this minimal implementation.
1 parent ed5228f commit cae8990

6 files changed

Lines changed: 27 additions & 12 deletions

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‎SQL/0000-00-05-ElectrophysiologyTables.sql‎

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@@ -54,6 +54,7 @@ CREATE TABLE `physiological_file` (
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`AcquisitionTime` DATETIME DEFAULT NULL,
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`InsertedByUser` VARCHAR(50) NOT NULL,
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`FilePath` VARCHAR(255) NOT NULL,
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`DownloadPath` VARCHAR(255) NOT NULL,
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`Index` INT(5) DEFAULT NULL,
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`ParentID` INT(10) unsigned DEFAULT NULL,
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`HeadShapeFileID` INT(10) unsigned DEFAULT NULL,

‎SQL/New_patches/2026-03-13_physio-file-download-path.sql‎

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-- Add the column as nullable first.
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ALTER TABLE `physiological_file`
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ADD COLUMN `DownloadPath` VARCHAR(255) DEFAULT NULL AFTER `FilePath`;
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-- Populate the download path using the file path value.
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UPDATE `physiological_file`
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SET `DownloadPath` = `FilePath`;
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-- Add the non-null constraint once the data is populated.
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ALTER TABLE `physiological_file`
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MODIFY COLUMN `DownloadPath` VARCHAR(255) NOT NULL;

‎modules/electrophysiology_browser/php/models/electrophysiofile.class.inc‎

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@@ -52,7 +52,8 @@ class ElectrophysioFile implements \LORIS\Data\DataInstance
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FileType,
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AcquisitionTime,
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InsertedByUser,
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FilePath
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FilePath,
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DownloadPath
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FROM physiological_file
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LEFT JOIN physiological_modality as pm
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USING (PhysiologicalModalityID)

‎modules/electrophysiology_browser/php/sessions.class.inc‎

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@@ -671,7 +671,7 @@ class Sessions extends \NDB_Page
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function getPhysioFileDownloadlinks(ElectrophysioFile $physioFileObj): array
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{
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$physioFileID = $physioFileObj->getParameter('PhysiologicalFileID');
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$physioFile = $physioFileObj->getParameter('FilePath');
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$physioFile = $physioFileObj->getParameter('DownloadPath');
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$db = $this->loris->getDatabaseConnection();
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$downloadLinks = [];
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‎modules/electrophysiology_browser/test/EEGBrowserIntegrationTest.php‎

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@@ -124,6 +124,7 @@ function setUp(): void
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'PhysiologicalOutputTypeID' => 22,
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'InsertedByUser' => 'Unit Tester',
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'FilePath' => '/path/to/test/file',
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'DownloadPath' => '/path/to/test/file',
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'FileType' => 'testType'
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]
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);
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'PhysiologicalOutputTypeID' => 23,
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'InsertedByUser' => 'Unit Tester',
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'FilePath' => '/path/to/test/file2',
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'DownloadPath' => '/path/to/test/file2.tar',
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'FileType' => 'testType2'
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]
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);

‎raisinbread/RB_files/RB_physiological_file.sql‎

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@@ -1,15 +1,15 @@
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SET FOREIGN_KEY_CHECKS=0;
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TRUNCATE TABLE `physiological_file`;
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LOCK TABLES `physiological_file` WRITE;
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (1,1,1,167,'2019-08-21 15:09:57','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (2,1,1,168,'2019-08-21 15:10:06','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT168/ses-V1/eeg/sub-OTT168_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (3,1,1,174,'2019-08-21 15:10:13','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT174/ses-V1/eeg/sub-OTT174_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (4,1,1,176,'2019-08-21 15:10:21','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT176/ses-V1/eeg/sub-OTT176_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (5,1,1,175,'2019-08-21 15:10:36','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT175/ses-V1/eeg/sub-OTT175_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (6,1,1,172,'2019-08-21 15:10:43','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT172/ses-V1/eeg/sub-OTT172_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (7,1,1,170,'2019-08-21 15:10:49','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT170/ses-V1/eeg/sub-OTT170_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (8,1,1,173,'2019-08-21 15:10:57','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT173/ses-V1/eeg/sub-OTT173_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (9,1,1,171,'2019-08-21 15:11:07','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT171/ses-V1/eeg/sub-OTT171_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (10,1,1,166,'2019-08-21 15:11:21','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT166/ses-V1/eeg/sub-OTT166_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (1,1,1,167,'2019-08-21 15:09:57','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (2,1,1,168,'2019-08-21 15:10:06','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT168/ses-V1/eeg/sub-OTT168_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT168/ses-V1/eeg/sub-OTT168_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (3,1,1,174,'2019-08-21 15:10:13','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT174/ses-V1/eeg/sub-OTT174_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT174/ses-V1/eeg/sub-OTT174_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (4,1,1,176,'2019-08-21 15:10:21','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT176/ses-V1/eeg/sub-OTT176_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT176/ses-V1/eeg/sub-OTT176_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (5,1,1,175,'2019-08-21 15:10:36','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT175/ses-V1/eeg/sub-OTT175_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT175/ses-V1/eeg/sub-OTT175_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (6,1,1,172,'2019-08-21 15:10:43','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT172/ses-V1/eeg/sub-OTT172_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT172/ses-V1/eeg/sub-OTT172_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (7,1,1,170,'2019-08-21 15:10:49','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT170/ses-V1/eeg/sub-OTT170_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT170/ses-V1/eeg/sub-OTT170_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (8,1,1,173,'2019-08-21 15:10:57','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT173/ses-V1/eeg/sub-OTT173_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT173/ses-V1/eeg/sub-OTT173_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (9,1,1,171,'2019-08-21 15:11:07','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT171/ses-V1/eeg/sub-OTT171_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT171/ses-V1/eeg/sub-OTT171_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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INSERT INTO `physiological_file` (`PhysiologicalFileID`, `PhysiologicalModalityID`, `PhysiologicalOutputTypeID`, `SessionID`, `InsertTime`, `FileType`, `AcquisitionTime`, `InsertedByUser`, `FilePath`, `DownloadPath`, `Index`, `ParentID`, `HeadShapeFileID`) VALUES (10,1,1,166,'2019-08-21 15:11:21','edf',NULL,'cecile','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT166/ses-V1/eeg/sub-OTT166_ses-V1_task-faceO_eeg.edf','bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT166/ses-V1/eeg/sub-OTT166_ses-V1_task-faceO_eeg.edf',NULL,NULL,NULL);
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UNLOCK TABLES;
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SET FOREIGN_KEY_CHECKS=1;

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