diff --git a/README.md b/README.md index 7a1e039..8e4eb72 100644 --- a/README.md +++ b/README.md @@ -53,8 +53,9 @@ Running DICAT will open a window with three different tabs: ### Using DICAT executables/applications Executables of DICAT have been created for most systems and can be found with -each release of DICAT in the Github repository. Download the executable -relevant to your system and move it to any folder of your choice. +each [release](https://github.com/aces/DICAT/releases) of DICAT in the Github +repository. Download the executable relevant to your system and move it to any +folder of your choice. To open DICAT, simply double click on the executable. @@ -65,7 +66,7 @@ Windows OS. ###### Requirements -Before running DICAT, make sure your systems contains a +Before running DICAT, make sure your system contains a [Python](https://www.python.org) compiler with the [TkInter](https://wiki.python.org/moin/TkInter) library (usually, TkInter comes by default with most Python installations). @@ -106,17 +107,18 @@ Once a directory containing DICOM files have been selected (as described in the above section), the DICOM fields can be viewed when clicking on the *“View DICOM fields”* button (3). -The DICOM fields will be displayed in a table with editable fields in black (4) -and non-editable fields greyed out (5). The non-editable fields will be -replaced by empty strings in the DICOM files when running the de-identification, -while the editable fields will be replaced by the value entered by the user. -By default, editable fields are *“PatientName”*, *“PatientBirthDate”* and -*“PatientSex”*. - -The *“Clear”* button (6) will erase values from all editable fields. +The DICOM identifiable fields will be displayed in a table with editable fields (4). + +Users can choose to delete all identifiable fields using the *“Clear All Fields”* +button (5). + +Users can also directly edit the fields (6) in the table and all values present in +the table will be inserted into the corresponding DICOM fields in the imaging files. +> Note that the PatientName field is required (7) and will need to be filled +with new IDs in order to label the scan for that session. Finally, once the user has finalized the edits, clicking on the *“De-identify”* -button (7) will run the de-identification tool on the DICOM dataset. +button (8) will run the de-identification tool on the DICOM dataset. ***Mass DICOM de-identification using `mass_deidentify.py`*** @@ -165,7 +167,7 @@ column headers (10). ## Authors -Ayan Sengupta - Concept, DICOM-toolkit implementation, Pydicom implementation +Ayan Sengupta - Concept, Pydicom implementation Cecile Madjar - GUI implementation, PyDICOM implementation, python integration of DICOM-toolkit, ID key diff --git a/dicat/mass_deidentify.py b/dicat/mass_deidentify.py index 7d66c9f..fdda8c6 100644 --- a/dicat/mass_deidentify.py +++ b/dicat/mass_deidentify.py @@ -10,8 +10,8 @@ def main(): usage = ( 'usage : mass_deidentify -c \n\n' 'options: \n' - '\t-c, --csvfile: CSV file with the following format\n' - '\t-x, --xmlfile: XML file with the list of DICOM fields to zap\n' + '\t-c, --csvfile: path to the CSV file with the following format\n' + '\t-x, --xmlfile: path to the XML file with the list of DICOM fields to zap\n' '\t-v, --verbose: if set, be verbose. Note: regardless of whether the\n' '\t verbose option is set, a summary of success/failure\n' '\t will be provided at the end of execution.\n\n' diff --git a/docs/images/DICOM_deidentification.png b/docs/images/DICOM_deidentification.png index 9a27719..5fbd9f2 100644 Binary files a/docs/images/DICOM_deidentification.png and b/docs/images/DICOM_deidentification.png differ diff --git a/docs/images/mass_deidentify_help.png b/docs/images/mass_deidentify_help.png index 64d831f..090d2da 100644 Binary files a/docs/images/mass_deidentify_help.png and b/docs/images/mass_deidentify_help.png differ