diff --git a/docs/scripts_md/ConfigOB.md b/docs/scripts_md/ConfigOB.md index fe21eb2fb..a4beb3138 100644 --- a/docs/scripts_md/ConfigOB.md +++ b/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. diff --git a/docs/scripts_md/DBI.md b/docs/scripts_md/DBI.md index ce1a61781..38fdfab22 100644 --- a/docs/scripts_md/DBI.md +++ b/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 - - $name: name of the config setting - -RETURNS: value corresponding to the config setting in the `Config` table - of LORIS - # TO DO Expand the package with more functions. diff --git a/docs/scripts_md/ImagingUpload.md b/docs/scripts_md/ImagingUpload.md index f872b3606..b114f8a0a 100644 --- a/docs/scripts_md/ImagingUpload.md +++ b/docs/scripts_md/ImagingUpload.md @@ -90,6 +90,12 @@ successfully. RETURNS: 1 on success, 0 on failure +### runPythonArchiveLoader() + +This methods will call `run_dicom_archive_loader.py` + +RETURNS: 1 on success, 0 on failure + ### DicomPatientNameMatch($dicom\_file, $expected\_pname\_regex) This method extracts the patient name field from the DICOM file header using diff --git a/docs/scripts_md/MRIProcessingUtility.md b/docs/scripts_md/MRIProcessingUtility.md index b90d19911..d049c65b7 100644 --- a/docs/scripts_md/MRIProcessingUtility.md +++ b/docs/scripts_md/MRIProcessingUtility.md @@ -329,7 +329,7 @@ INPUTS: RETURNS: acquisition protocol ID of the MINC file -### dicom\_to\_minc($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. @@ -337,7 +337,7 @@ 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.