aces · maximemulder · Jun 26, 2024
diff --git a/DTIPrep/DTIPrepRegister.pl b/DTIPrep/DTIPrepRegister.pl
diff --git a/docs/02-Install.md b/docs/02-Install.md
diff --git a/docs/03-TechnicalInfrastructure.md b/docs/03-TechnicalInfrastructure.md
diff --git a/docs/scripts_md/GetRole.md b/docs/scripts_md/GetRole.md
@@ -7,11 +7,11 @@ NeuroDB::objectBroker::GetRole -- A role for basic SELECT operations on the data
 # DESCRIPTION
 
 This class provides methods used to accomplish basic `SELECT` operations on the database.
-It allows the retrieval of records using a simple `WHERE` clause of the form 
+It allows the retrieval of records using a simple `WHERE` clause of the form
 `WHERE constraint_1 AND constraint_2 AND ... AND constraint_n`.
-Subparts of the `WHERE` clause can only be combined with `AND` (`OR` is not supported). 
-Each subpart of the `WHERE` clause specifies that a field must be either equal to a given 
-value, not equal to a given value, NULL or NOT NULL. 
+Subparts of the `WHERE` clause can only be combined with `AND` (`OR` is not supported).
+Each subpart of the `WHERE` clause specifies that a field must be either equal to a given
+value, not equal to a given value, NULL or NOT NULL.
 
 Classes using this role must implement methods `getColumnNames()`, `getTableName()` and `db()`.
 
@@ -20,7 +20,7 @@ Classes using this role must implement methods `getColumnNames()`, `getTableName
 ### get($isCount, $columnValuesRef)
 
 Fetches the records in the table whose name is returned by method `getTableName()` that satisfy
-specific constraints. 
+specific constraints.
 
 Note that this method is private.
 
@@ -31,21 +31,21 @@ INPUTS:
      should have in order to be part of the result set (key: column name, value: column
      value).
 
-RETURNS: 
+RETURNS:
    - a reference to an array of hash references. Every hash contains the values
      for a given row returned by the method call: the key/value pairs contain
-     the name of a column (see `@MRI_SCAN_TYPE_FIELDS`) and the value it 
+     the name of a column (see `@MRI_SCAN_TYPE_FIELDS`) and the value it
      holds, respectively. As an example, suppose array `$r` contains the result of a
-     given call to this function. One would fetch the `Scan_type` of the 2nd record 
-     returned using `$r->[1]->{'Scan_type'}`.
+     given call to this function. One would fetch the `MriScanTypeName` of the 2nd record
+     returned using `$r->[1]->{'MriScanTypeName'}`.
      If the method is called with `$isCount` set to true, then it will return
-     a reference to an array containing a single hash reference, its unique key being 
+     a reference to an array containing a single hash reference, its unique key being
      `'COUNT(*)'` with the associated value set to the selected count.
 
 ### addWhereEquals($columnValuesRef, $k, $whereRef, $valsRef)
 
 Gets the string representation of a constraint of the form `field=value` and adds it
-to the current set of `WHERE` clauses. Note that constraints specifying that a field 
+to the current set of `WHERE` clauses. Note that constraints specifying that a field
 must be NULL will be properly translated to `field IS NULL` (not `field=NULL`).
 
 INPUTS:
@@ -55,13 +55,13 @@ INPUTS:
    - Reference on the array of values each field in `$columnValuesRef` must be
      equal or not equal to.
 
-RETURNS: 
+RETURNS:
    - Nothing (adds an element to `@$whereRef`).
 
 ### addWhereFunction($columnValuesRef, $k, $whereRef, $valsRef)
 
 Gets the string representation of a constraint that uses an SQL function or operator.
-Currently, only the operator `NOT` (i.e. field `NOT` equal to a given value or `NOT NULL`) is 
+Currently, only the operator `NOT` (i.e. field `NOT` equal to a given value or `NOT NULL`) is
 supported.
 
 INPUTS:
@@ -71,13 +71,13 @@ INPUTS:
    - Reference on the array of values each field in `$columnValuesRef` must be
      equal or not equal to.
 
-RETURNS: 
+RETURNS:
    - Nothing. Updates arrays `@$whereRef` (and `@$valsRef` if necessary).
 
 ### addWhereNotEquals($columnValuesRef, $k, $whereRef, $valsRef)
 
 Gets the string representation of a constraint of the form `field != value` and adds it to
-the current set of `WHERE` clauses. Note that constraints specifying that a field must not be NULL 
+the current set of `WHERE` clauses. Note that constraints specifying that a field must not be NULL
 will be properly translated to `field IS NOT NULL` (not `field!=NULL`).
 
 INPUTS:
@@ -87,13 +87,13 @@ INPUTS:
    - Reference on the array of values each field in `$columnValuesRef` must be
      equal or not equal to.
 
-RETURNS: 
+RETURNS:
    - Nothing. Updates arrays `@$whereRef` (and `@$valsRef` if necessary).
 
 ### get($columnValuesRef)
 
 Fetches the records in the table whose name is returned by method `getTableName()` that satisfy
-specific constraints. 
+specific constraints.
 
 INPUTS:
    - reference to a hash array that contains the constraints on the column values that the records
@@ -102,25 +102,25 @@ INPUTS:
      a single value or a reference to a hash (this hash describes a constraint involving an
      SQL function or operator other than '='). Examples of a valid set of constraints:
 
-     {  
+     {
        Field1 => 'Value1',
        Field2 => { NOT => 3 },
        Field3 => undef
      }
-
 
-RETURNS: 
+
+RETURNS:
    - a reference to an array of hash references. Every hash contains the values
      for a given row returned by the method call: the key/value pairs contain
-     the name of a column (as listed by `getColumnNames()`) and the value it 
+     the name of a column (as listed by `getColumnNames()`) and the value it
      holds, respectively. As an example, suppose array `$r` contains the result of a
-     given call to this function. One would fetch the `Scan_type` of the 2nd record 
-     returned using `$r->[1]->{'Scan_type'}`.
+     given call to this function. One would fetch the `MriScanTypeName` of the 2nd record
+     returned using `$r->[1]->{'MriScanTypeName'}`.
 
 ### getCount($columnValuesRef)
 
-Fetches the number of records in the table whose name is returned by method `getTableName()` 
-that satisfy specific constraints. 
+Fetches the number of records in the table whose name is returned by method `getTableName()`
+that satisfy specific constraints.
 
 INPUTS:
    - reference to a hash array that contains the constraints on the column values that the records
@@ -129,12 +129,12 @@ INPUTS:
      a single value or a reference to a hash (this hash describes a constraint involving an
      SQL function or operator other than '='). Examples of a valid set of constraints:
 
-     {  
+     {
        Field1 => 'Value1',
        Field2 => { NOT => 3 },
        Field3 => undef
      }
-
 
-RETURNS: 
+
+RETURNS:
    - the number of records found.
diff --git a/docs/scripts_md/MriScanTypeOB.md b/docs/scripts_md/MriScanTypeOB.md
@@ -77,12 +77,12 @@ INPUTS:
 
 RETURNS: a reference to an array of hash references. Every hash contains the values
         for a given row returned by the method call: the key/value pairs contain
-        the name of a column (see `@MRI_SCAN_TYPE_FIELDS`) and the value it 
+        the name of a column (see `@MRI_SCAN_TYPE_FIELDS`) and the value it
         holds, respectively. As an example, suppose array `$r` contains the result of a
-        given call to this function. One would fetch the `Scan_type` of the 2nd record 
-        returned using `$r-`\[1\]->{'Scan\_type'}>.
+        given call to this function. One would fetch the `MriScanTypeName` of the 2nd record
+        returned using `$r-`\[1\]->{'MriScanTypeName'}>.
         If the method is called with `$isCount` set to true, then it will return
-        a reference to an array containing a single hash reference, its unique key being 
+        a reference to an array containing a single hash reference, its unique key being
         `'COUNT(*)'` with the associated value set to the selected count.
 
 # TO DO

diff --git a/docs/scripts_md/minc_to_bids_converter.md b/docs/scripts_md/minc_to_bids_converter.md
@@ -73,30 +73,30 @@ RETURNS:
 
     {
         "1" => {
-            'fileID'                => 'FileID value',
-            'file'                  => 'file path',
-            'echoTime'              => 'Echo Time of the file',
-            'AcquisitionProtocolID' => 'Scan type ID',
-            'candID'                => 'Candidate CandID',
-            'sessionID'             => 'Session ID',
-            'visitLabel'            => 'Visit Label',
-            'echoNumber'            => 'Echo Number of the scan',
-            'seriesNumber'          => 'Series Number of the scan',
-            'imageType'             => 'Image Type',
-            'lorisScanType'         => 'LORIS Scan Type name'
+            'fileID'        => 'FileID value',
+            'file'          => 'file path',
+            'echoTime'      => 'Echo Time of the file',
+            'MriScanTypeID' => 'Scan type ID',
+            'candID'        => 'Candidate CandID',
+            'sessionID'     => 'Session ID',
+            'visitLabel'    => 'Visit Label',
+            'echoNumber'    => 'Echo Number of the scan',
+            'seriesNumber'  => 'Series Number of the scan',
+            'imageType'     => 'Image Type',
+            'lorisScanType' => 'LORIS Scan Type name'
         },
         "2" => {
-            'fileID'                => 'FileID value',
-            'file'                  => 'file path',
-            'echoTime'              => 'Echo Time of the file',
-            'AcquisitionProtocolID' => 'Scan type ID',
-            'candID'                => 'Candidate CandID',
-            'sessionID'             => 'Session ID',
-            'visitLabel'            => 'Visit Label',
-            'echoNumber'            => 'Echo Number of the scan',
-            'seriesNumber'          => 'Series Number of the scan',
-            'imageType'             => 'Image Type',
-            'lorisScanType'         => 'LORIS Scan Type name'
+            'fileID'        => 'FileID value',
+            'file'          => 'file path',
+            'echoTime'      => 'Echo Time of the file',
+            'MriScanTypeID' => 'Scan type ID',
+            'candID'        => 'Candidate CandID',
+            'sessionID'     => 'Session ID',
+            'visitLabel'    => 'Visit Label',
+            'echoNumber'    => 'Echo Number of the scan',
+            'seriesNumber'  => 'Series Number of the scan',
+            'imageType'     => 'Image Type',
+            'lorisScanType' => 'LORIS Scan Type name'
         }
         ...
     }
@@ -162,7 +162,7 @@ OUTPUT:
         'BIDSCategoryName'        => 'BIDS category to use for the NIfTI file, aka anat, func, fmap, dwi...',
         'BIDSScanTypeSubCategory' => 'BIDS subcategory to use for the NIfTI file, aka task-rest, task-memory...',
         'BIDSEchoNumber'          => 'Echo Number associated with the NIfTI file',
-        'Scan_type'               => 'label of the LORIS Scan type from the mri_scan_type table'
+        'ScanType'                => 'label of the LORIS Scan type from the mri_scan_type table'
     }
 
 Note: BIDSEchoNumber and BIDSScanTypeSubCategory can be null for a given NIfTI file.
@@ -371,14 +371,14 @@ OUTPUT:
 
 ### grep\_acquisitionProtocolID\_from\_BIDS\_scan\_type($db\_handle, $bids\_scan\_type)
 
-Greps the AcquisitionProtocolID associated to a BIDS magnitude file in the database.
+Greps the MriScanTypeID associated to a BIDS magnitude file in the database.
 
 INPUTS:
     - $db\_handle     : database handle
     - $bids\_scan\_type: name of the BIDS scan type (for example: magnitude)
 
 OUTPUT:
-    - AcquisitionProtocolID associated to the BIDS scan type file in the database
+    - MriScanTypeID associated to the BIDS scan type file in the database
 
 ### create\_BIDS\_magnitude\_files($phasediff\_filename, $magnitude\_files\_hash)
 

diff --git a/docs/scripts_md/register_processed_data.md b/docs/scripts_md/register_processed_data.md
@@ -71,7 +71,7 @@ RETURNS: scanner ID
 
 ### getAcqProtID($scanType, $dbh)
 
-This function returns the `AcquisitionProtocolID` of the file to register in
+This function returns the `MriScanTypeID` of the file to register in
 the database based on `scanType` in the `mri_scan_type` table.
 
 INPUTS:

diff --git a/python/lib/database_lib/files.py b/python/lib/database_lib/files.py
@@ -139,20 +139,20 @@ def update_files(self, file_id, fields, values):
 
     def select_distinct_acquisition_protocol_id_per_tarchive_source(self, tarchive_id):
         """
-        Get a list of distinct scan types (a.k.a. `AcquisitionProtocolID`) inserted into the `files`
+        Get a list of distinct scan types (a.k.a. `MriScanTypeID`) inserted into the `files`
         table for a given DICOM archive (a.k.a. `TarchiveSource`).
 
         :param tarchive_id: `TarchiveID` to use as the `TarchiveSource` to restrict the SELECT statement on
          :type tarchive_id: int
 
-        :return: list of scan types found (`AcquisitionProtocolID`)
+        :return: list of scan types found (`MriScanTypeID`)
          :rtype: list
         """
 
-        query = "SELECT DISTINCT AcquisitionProtocolID FROM files WHERE TarchiveSource = %s"
+        query = "SELECT DISTINCT MriScanTypeID FROM files WHERE TarchiveSource = %s"
 
         results = self.db.pselect(query=query, args=(tarchive_id,))
-        acquisition_protocol_id_list = [v["AcquisitionProtocolID"] for v in results]
+        acquisition_protocol_id_list = [v["MriScanTypeID"] for v in results]
 
         return acquisition_protocol_id_list
 
@@ -166,15 +166,15 @@ def get_file_ids_and_series_number_per_scan_type_and_tarchive_id(self, tarchive_
         :param scan_type_id: ID of the scan type to restrict the query on
          :type scan_type_id: int
 
-        :return: list of `FileID` and `SeriesNumber` for a given `TarchiveID` and `AcquisitionProtocolID`
+        :return: list of `FileID` and `SeriesNumber` for a given `TarchiveID` and `MriScanTypeID`
          :rtype: list
         """
 
         query = "SELECT FileID, Value AS SeriesNumber " \
                 "FROM files " \
                 "  JOIN parameter_file USING(FileID) " \
                 "  JOIN parameter_type USING(ParameterTypeID) " \
-                "WHERE TarchiveSource = %s AND AcquisitionProtocolID = %s AND Name = %s"
+                "WHERE TarchiveSource = %s AND MriScanTypeID = %s AND Name = %s"
 
         return self.db.pselect(query=query, args=(tarchive_id, scan_type_id, "series_number"))
 

diff --git a/python/lib/database_lib/mri_protocol.py b/python/lib/database_lib/mri_protocol.py
@@ -112,15 +112,15 @@ def get_bids_info_for_scan_type_id(self, scan_type_id):
                 bids_scan_type.BIDSScanType,
                 bmstr.BIDSEchoNumber,
                 bids_phase_encoding_direction.BIDSPhaseEncodingDirectionName,
-                mst.Scan_type
+                mst.MriScanTypeName AS ScanType
             FROM bids_mri_scan_type_rel bmstr
-                JOIN      mri_scan_type mst             ON mst.ID = bmstr.MRIScanTypeID
+                JOIN      mri_scan_type mst             ON mst.MriScanTypeID = bmstr.MRIScanTypeID
                 JOIN      bids_category                 USING (BIDSCategoryID)
                 JOIN      bids_scan_type                USING (BIDSScanTypeID)
                 LEFT JOIN bids_scan_type_subcategory    USING (BIDSScanTypeSubCategoryID)
                 LEFT JOIN bids_phase_encoding_direction USING (BIDSPhaseEncodingDirectionID)
             WHERE
-                mst.ID = %s
+                mst.MriScanTypeID = %s
         """
 
         results = self.db.pselect(query=query, args=(scan_type_id,))

diff --git a/python/lib/database_lib/mri_protocol_checks.py b/python/lib/database_lib/mri_protocol_checks.py
@@ -56,7 +56,7 @@ def get_list_of_possible_protocols_based_on_session_info(
 
         query = "SELECT * FROM mri_protocol_checks" \
                 " JOIN mri_protocol_checks_group_target mpcgt USING (MriProtocolChecksGroupID)" \
-                " WHERE Scan_type = %s "
+                " WHERE MriScanTypeID = %s "
 
         query += " AND (mpcgt.ProjectID IS NULL OR mpcgt.ProjectID = %s)" \
             if project_id else " AND mpcgt.ProjectID IS NULL"

diff --git a/python/lib/database_lib/mri_scan_type.py b/python/lib/database_lib/mri_scan_type.py
@@ -47,11 +47,11 @@ def get_scan_type_name_from_id(self, scan_type_id):
         """
 
         results = self.db.pselect(
-            query='SELECT Scan_type FROM mri_scan_type WHERE ID = %s',
+            query='SELECT MriScanTypeName FROM mri_scan_type WHERE MriScanTypeID = %s',
             args=(scan_type_id,)
         )
 
-        return results[0]['Scan_type'] if results else None
+        return results[0]['MriScanTypeName'] if results else None
 
     def get_scan_type_id_from_name(self, scan_type_name):
         """
@@ -65,8 +65,8 @@ def get_scan_type_id_from_name(self, scan_type_name):
         """
 
         results = self.db.pselect(
-            query='SELECT ID FROM mri_scan_type WHERE Scan_type = %s',
+            query='SELECT MriScanTypeID FROM mri_scan_type WHERE MriScanTypeName = %s',
             args=(scan_type_name,)
         )
 
-        return results[0]['ID'] if results else None
+        return results[0]['MriScanTypeID'] if results else None
diff --git a/python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py b/python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py
@@ -625,7 +625,7 @@ def _register_violations_log(self, violations_list, file_rel_path):
             'PatientName': self.subject_info.name,
             'CandID': self.subject_info.cand_id,
             'Visit_label': self.subject_info.visit_label,
-            'Scan_type': self.scan_type_id,
+            'MriScanTypeID': self.scan_type_id,
             'EchoTime': scan_param['EchoTime'] if 'EchoTime' in scan_param.keys() else None,
             'EchoNumber': scan_param['EchoNumber'] if 'EchoNumber' in scan_param.keys() else None,
             'PhaseEncodingDirection': phase_enc_dir,
@@ -667,7 +667,7 @@ def _register_into_files_and_parameter_file(self, nifti_rel_path):
             'PhaseEncodingDirection': phase_enc_dir,
             'CoordinateSpace': 'native',
             'OutputType': 'native',
-            'AcquisitionProtocolID': self.scan_type_id,
+            'MriScanTypeID': self.scan_type_id,
             'FileType': file_type,
             'InsertedByUserID': getpass.getuser(),
             'InsertTime': datetime.datetime.now().timestamp(),