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createVisit/Project/Subproject imaging config
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@laemtl
laemtl committed Feb 18, 2023
1 parent 63aaa70 commit 982edb0
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37 changes: 20 additions & 17 deletions SQL/0000-00-03-ConfigTables.sql
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Expand Up @@ -82,7 +82,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('gui', 'Settings related to the overall display of LORIS', 1, 0, 'GUI', 3);
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'css', 'CSS file used for rendering (default main.css)', 1, 0, 'text', ID, 'CSS file', 1 FROM ConfigSettings WHERE Name="gui";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'rowsPerPage', 'Number of table rows to display per page', 1, 0, 'text', ID, 'Table rows per page', 2 FROM ConfigSettings WHERE Name="gui";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'StudyDescription', 'Description of the Study', 1, 0, 'textarea', ID , 'Study Description', 2 FROM ConfigSettings WHERE Name="gui";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'StudyDescription', 'Description of the Study', 1, 0, 'textarea', ID , 'Study Description', 3 FROM ConfigSettings WHERE Name="gui";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useEEGBrowserVisualizationComponents', 'Whether to enable the visualization components on the EEG Browser module', 1, 0, 'boolean', ID, 'Enable the EEG Browser components', 4 FROM ConfigSettings WHERE Name="gui";


Expand Down Expand Up @@ -139,22 +139,25 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'DICOM converter tool to use (dcm2mnc or dcm2niix)', 7 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 8 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'DICOM field (either PatientName or PatientID) to use to get the patient identifiers and the center name of the DICOM study', 1, 0, 'lookup_center', ID, 'Patient identifiers and center name lookup variable', 9 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Enable candidate creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Upload creation of candidates', 10 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Enable use of batch management in the imaging pipeline', 1, 0, 'boolean', ID, 'Project batch management used', 11 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 13 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 14 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 15 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 16 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 17 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'excluded_series_description', 'Series description to be excluded from insertion into the database (typically localizers and scouts)', 1, 1, 'text', ID, 'Series description to exclude from imaging insertion', 18 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'ComputeDeepQC', 'Determines whether a call is made from LORIS-MRI to the DeepQC app for automatic QC prediction', 1, 0, 'boolean', ID, 'Compute automatic QC', 18 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriConfigFile', 'Name of the Perl MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Perl MRI config file', 19 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EnvironmentFile', 'Name of the environment file that need to be sourced for the imaging pipeline', 1, 0, 'text', ID, 'Name of the environment file', 20 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'compute_snr_modalities', 'Modalities for which the SNR should be computed when running the insertion MRI scripts', 1, 1, 'scan_type', ID, 'Modalities on which SNR should be calculated', 21 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reference_scan_type_for_defacing', 'Scan type to use as a reference for registration when defacing anatomical images (typically a T1W image)', 1, 0, 'scan_type', ID, 'Scan type to use as a reference for defacing (typically a T1W image)', 22 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'modalities_to_deface', 'Modalities for which defacing should be run and defaced image inserted in the database', 1, 1, 'scan_type', ID, 'Modalities on which to run the defacing pipeline', 23 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_bids_vl', 'Default visit label to use when no visit label set in the BIDS dataset', 1, 0, 'text', ID, 'Default visit label for BIDS dataset', 24 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriPythonConfigFile', 'Name of the Python MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Python MRI config file', 25 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Enable candidate creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Enable candidate creation', 10 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createVisit', 'Enable visit creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Enable visit creation', 11 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_project', 'Default project used when creating scan candidate or visit', 1, 0, 'text', ID, 'Default project', 12 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_subproject', 'Default subproject used when creating scan visit', 1, 0, 'text', ID, 'Default subproject', 13 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_bids_vl', 'Default visit label to use when no visit label set in the BIDS dataset', 1, 0, 'text', ID, 'Default visit label for BIDS dataset', 14 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Enable use of batch management in the imaging pipeline', 1, 0, 'boolean', ID, 'Project batch management used', 15 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 16 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 17 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 18 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 19 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 20 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'excluded_series_description', 'Series description to be excluded from insertion into the database (typically localizers and scouts)', 1, 1, 'text', ID, 'Series description to exclude from imaging insertion', 21 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'ComputeDeepQC', 'Determines whether a call is made from LORIS-MRI to the DeepQC app for automatic QC prediction', 1, 0, 'boolean', ID, 'Compute automatic QC', 22 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriConfigFile', 'Name of the Perl MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Perl MRI config file', 23 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EnvironmentFile', 'Name of the environment file that need to be sourced for the imaging pipeline', 1, 0, 'text', ID, 'Name of the environment file', 24 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'compute_snr_modalities', 'Modalities for which the SNR should be computed when running the insertion MRI scripts', 1, 1, 'scan_type', ID, 'Modalities on which SNR should be calculated', 25 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reference_scan_type_for_defacing', 'Scan type to use as a reference for registration when defacing anatomical images (typically a T1W image)', 1, 0, 'scan_type', ID, 'Scan type to use as a reference for defacing (typically a T1W image)', 26 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'modalities_to_deface', 'Modalities for which defacing should be run and defaced image inserted in the database', 1, 1, 'scan_type', ID, 'Modalities on which to run the defacing pipeline', 27 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriPythonConfigFile', 'Name of the Python MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Python MRI config file', 28 FROM ConfigSettings WHERE Name="imaging_pipeline";

-- MINC to BIDS converter settings
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('minc2bids', 'Settings related to converting MINC to BIDS LORIS-MRI tool script', 1, 0, 'MINC to BIDS Converter Tool Options', 13);
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21 changes: 21 additions & 0 deletions SQL/New_patches/2023-02-17-imaging-new-config.sql
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@@ -0,0 +1,21 @@
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createVisit', 'Enable visit creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Enable visit creation', 11 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_project', 'Default project used when creating scan candidate or visit', 1, 0, 'text', ID, 'Default project', 12 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_subproject', 'Default subproject used when creating scan visit', 1, 0, 'text', ID, 'Default subproject', 13 FROM ConfigSettings WHERE Name="imaging_pipeline";

UPDATE ConfigSettings SET Label = 'Enable candidate creation' WHERE Name = 'createCandidates';

UPDATE ConfigSettings SET OrderNumber = 14 WHERE Name = 'default_bids_vl';
UPDATE ConfigSettings SET OrderNumber = 15 WHERE Name = 'is_qsub';
UPDATE ConfigSettings SET OrderNumber = 16 WHERE Name = 'DTI_volumes';
UPDATE ConfigSettings SET OrderNumber = 17 WHERE Name = 't1_scan_type';
UPDATE ConfigSettings SET OrderNumber = 18 WHERE Name = 'reject_thresh';
UPDATE ConfigSettings SET OrderNumber = 19 WHERE Name = 'niak_path';
UPDATE ConfigSettings SET OrderNumber = 20 WHERE Name = 'QCed2_step';
UPDATE ConfigSettings SET OrderNumber = 21 WHERE Name = 'excluded_series_description';
UPDATE ConfigSettings SET OrderNumber = 22 WHERE Name = 'ComputeDeepQC';
UPDATE ConfigSettings SET OrderNumber = 23 WHERE Name = 'MriConfigFile';
UPDATE ConfigSettings SET OrderNumber = 24 WHERE Name = 'EnvironmentFile';
UPDATE ConfigSettings SET OrderNumber = 25 WHERE Name = 'compute_snr_modalities';
UPDATE ConfigSettings SET OrderNumber = 26 WHERE Name = 'reference_scan_type_for_defacing';
UPDATE ConfigSettings SET OrderNumber = 27 WHERE Name = 'modalities_to_deface';
UPDATE ConfigSettings SET OrderNumber = 28 WHERE Name = 'MriPythonConfigFile';
4 changes: 4 additions & 0 deletions raisinbread/RB_files/RB_Config.sql
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Expand Up @@ -107,5 +107,9 @@ INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (118,118,'');
INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (119,119,'');
INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (120,120,'database_config.py');
INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (121,125,'false');
INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (121,126,'0');
INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (121,127,'');
INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (121,128,'');
INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (121,129,'');
UNLOCK TABLES;
SET FOREIGN_KEY_CHECKS=1;
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