perldoc

docs/scripts_md/ConfigOB.md

@@ -207,6 +207,43 @@ Get the compute\_snr\_modalities Config setting
 
 RETURN: an array (possibly empty) of the modality IDs (i.e t1w, etc..) for which to compute the SNR
 
+### getExcludedSeriesDescription()
+
+Get the excluded\_series\_description Config setting
+
+RETURN: an array (possibly empty) of the series description to exclude from import
+
+### getModalitiesToDeface()
+
+Get the modalities\_to\_deface Config setting
+
+RETURN: an array (possibly empty) of the modalities to run the defacing pipeline on
+
+### getBidsDatasetAuthors()
+
+Get the bids\_dataset\_authors Config setting
+
+RETURN: an array (possibly empty) of the authors to use for a BIDS dataset
+
+### getBidsAcknowledgmentsText()
+
+Get the bids\_acknowledgments\_text Config setting
+
+RETURN: an array (possibly empty) of the acknowledgment text to use for a BIDS dataset
+
+### getBidsReadmeText()
+
+Get the bids\_readme\_text Config setting
+
+RETURN: an array (possibly empty) of the README text to use for a BIDS dataset
+
+### getBidsValidatorOptionsToIgnore()
+
+Get the bids\_validator\_options\_to\_ignore Config setting
+
+RETURN: an array (possibly empty) of the BIDS validator options to ignore
+to use when creating a BIDS dataset
+
 # TO DO
 
 Nothing planned.

docs/scripts_md/DBI.md

@@ -35,18 +35,6 @@ INPUTS:
 
 RETURNS: DBI database handler when connection is successful
 
-### getConfigSetting($dbh, $name)
-
-This method fetches the value (`$value`) stored in the `Config` table for a
-specific config setting (`$name`) specified as an input.
-
-INPUTS:
-  - $dbh : database handler
-  - $name: name of the config setting
-
-RETURNS: value corresponding to the config setting in the `Config` table
-         of LORIS
-
 # TO DO
 
 Expand the package with more functions.

docs/scripts_md/ImagingUpload.md

@@ -90,6 +90,12 @@ successfully.
 
 RETURNS: 1 on success, 0 on failure
 
+### runPythonArchiveLoader()
+
+This methods will call `run_dicom_archive_loader.py`
+
+RETURNS: 1 on success, 0 on failure
+
 ### DicomPatientNameMatch($dicom\_file, $expected\_pname\_regex)
 
 This method extracts the patient name field from the DICOM file header using

docs/scripts_md/MRIProcessingUtility.md

@@ -329,15 +329,15 @@ INPUTS:
 
 RETURNS: acquisition protocol ID of the MINC file
 
-### dicom\_to\_minc($study\_dir, $converter, $get\_dicom\_info, $exclude, $mail\_user, $upload\_id)
+### dicom\_to\_minc($study\_dir, $converter, $get\_dicom\_info, @exclude, $mail\_user, $upload\_id)
 
 Converts a DICOM study into MINC files.
 
 INPUTS:
   - $study\_dir      : DICOM study directory to convert
   - $converter      : converter to be used
   - $get\_dicom\_info : get DICOM information setting from the `Config` table
-  - $exclude        : which files to exclude from the `dcm2mnc` command
+  - @exclude        : which files to exclude from the `dcm2mnc` command
   - $mail\_user      : mail of the user
   - $upload\_id      : upload ID of the study
 
@@ -514,6 +514,6 @@ Hey! **The above document had some coding errors, which are explained below:**
 
     =cut found outside a pod block.  Skipping to next block.
 
-- Around line 1880:
+- Around line 1883:
 
     =cut found outside a pod block.  Skipping to next block.