2.6. Dicom

DICOM = Digital Imaging and Communications in Medicine. Is a medical standard for distributing any kind of medical image.
flair has a capability to process the DICOM files with the use of the
pydicom
module (available as an add-on package for your OS distribution) and convert
them to FLUKA VOXEL and/or USRBIN compatible files. As well convert the
RTPLAN and RTDOSE to a full input for simulating a treatment planning.
The interface contains a tree browser on the left side that one needs to fill with the appropriate DICOM files. The tree browser is going to classify the files based on their modality and group them with the same SOP UID class
:
Add will allow you to insert DICOM files to the project
:
Will remove DICOM files from the project
Adding DICOM files in the project:
Click on the Add button. The following dialog will allow you to select
the files

Select a parent directory containing the dicom files, up to a “Depth” nesting of subfolders.
Warning
Do not increase a lot the depth as it can take considerable amount of time to scan the sub-folders.
2.6.1. Dynamic Tabs
:
Display information on the selected dataset Dicom
:
Show in a tabular text editor the dataset Editor
:
Graphical dicom viewer Viewer
:
Convert a CT/NM/PT scan to a voxels file Voxel
:
Visualize and compare RTDOSE with USRBIN and their DVH RTViewer
:
Convert an RTPLAN to input RTPlan
2.6.2. Dicom Information

Selecting tab Dicom will display some generic information on the
selected dicom dataset. The displayed information will depend on the selected
modality.
e.g. when selecting an RTSTRUCT it will calculated and display all ROIS and their respective volumes

2.6.3. Dicom Editor

Shows in a multi-list tree as text the data stored in the selected dataset. The Editor permits to change the value of the data and save the file.
For easier browsing you can filter and display only the items matching a specific filter pattern.
Selecting multiple datasets (Shift+Right click) on the dataset left-tree, the Editor will display the “common” entries of all datasets.
Entries that are varied will be marked with a small dice-character in-front.
With multiple selected files, changing an entry will change this entry to ALL selected datasets. Can be used to anonymize the selected datasets.
2.6.4. Slice Viewer

The viewer depending on the modality is able to show also the ROI information.
2.6.5. Voxel Generation

You can convert the CT scan and the associated RTSTRUCT to a voxel format to be read by FLUKA
1. Hounsfield Units:
You will need to provide a file containing the mapping mapping information on how to convert the DICOM units (normally Hounsfield) to materials.
This can be done by editing the table below and save it to a file.
Click on <new> to add a new Units range
- < Unit:
specify the upper limit (+1) of the range Every entry will correspond to a range from the previous upper limit until the current upper limit-1
- Material:
select any of the predefined FLUKA materials as well the ones in the Materials input loaded before
Optionally you can specify correction factors for the density and dE/dx
- Crho_min density correction factor to be applied on the
lower limit of the unit range
- Crho_max density correction factor to be applied on the
upper limit of the unit range
- CdEdx_rel_min relative correction factor on dE/dx for the
minimum unit in the range
- CdEdx_rel_max relative correction factor on dE/dx for the
maximum unit in the range
Note
The program will sort the Unit ranges in ascending order
The first entry will correspond to all units from the minimum in all slices to the upper limit defined by the user
All units above the last entry will be assigned to the same material as the last entry and a warning will be displayed on the output window
All intermediate units within a range will be scaled linearly
dE/dx is applied relative to the correction of density (negative WHAT(1) in CORRFACT)
2. RTSTRUCT and Material: This tab allows to override some structures with a fixed material e.g. Everything outside the skin convert to Vacuum

You need to fill in the Material override table a combinatorial operation of the rois.
select the material override, e.g. VACUUM
add pairs of operation operations and ROI Operation can be:
- +:
inside of the ROI
- -:
outside of the ROI
Buttons:
VOXEL:
Will create the voxel file
Card:
Will insert(or update) a VOXEL card in the input with the correct coordinates of the VOXEL
2.6.6. RTPlan creation

Allows the conversion of an RTPLAN dicom file to the equivalent multi-spot beam input for FLUKA.
Limitations:
Currently it can create the files for one fraction and it does not create the MLC structure in case of photon plans.
Beam model file: Optionally you can provide a beam model file with additional information on the beam, like momentum, angular and spatial spread per beam energy.
The program will create a list of SPOTBEAM
,
SPOTPOS
, SPOTDIR
, SPOTTRAN
cards converted to the patient orientation system. For each Beam it will create
a separate #include
file with all the necessary cards.
The normalization for each beam will created with a special #define
variables
that can be automatically used by the DVH converter and RTViewer
The program will tag all cards generated with a special variable in order to be able to delete and replace in case is needed.
2.6.7. RTViewer

is a module linked with the RTDOSE modality to allow the comparison of the planned dose vs the calculated dose from the MC. You can load any RTDOSE and any USRBIN as planned or calculated, provide the necessary normalization factor and compare the results.
When an RTDOSE or a USRBIN is loaded the program will try to automatically create the DVH histograms, provided a voxels file is present.