CLI-Manual.md

@@ -109,15 +109,17 @@ Options:
 
 ## Options further explanation
 
-### `<dicom folder>` 
+### <dicom folder>
 
 is the root folder where all DICOM files are stored. It is assumed that each subfolder corresponds to one patient.
 
-### `<report folder>`
+### <report folder>
 
 is the folder where the report files will be placed. If the folder does not exist, the tool will create it.
 
-### `--loris_folder`  folder path where the dcm files are reorganized for LORIS pipeline
+### --loris_folder 
+
+folder path where the dcm files are reorganized for LORIS pipeline
 
 For the LORIS pipeline the dcm files are reorganized and stored in a folder structure `<loris_folder>/<patientid>/<patientid_visitcount>`.
 All the dcm sequence files that belong to the same scanning session (visit) are stored in the common folder `<patientid_visitcount>`.