CLI-Manual.md

@@ -89,6 +89,19 @@ The schema could be saved in two formats:
 
 ``` shell
 Usage: qctool dicom <options> <dicom folder> <report folder>
+
+  This command produces a validation report for MRIs in <dicom folder>.
+
+  All MRI dcm files belonging to the same Patient MUST be in the same
+  subfolder in <dicom folder>.
+
+  The validation report files are stored in <report folder>.
+
+Options:
+  --loris_folder <loris input folder>
+                                  LORIS input folder where the dcm files in
+                                  <dicom folder> will be reorganized
+  --help                          Show this message and exit.
 ```
 
 `<dicom folder>` is the root folder where all DICOM files are stored. It is assumed that each subfolder corresponds to one patient.