# Run AngioTK

AngioTK tests rely on a handful of MRI files. Please note that due to legal restrictions, these are not available in the git repository.

Our examples consists of three sets of actual patients MRIs - two of them being split, showing arteries and veins in disctinct MRI files - and one plastic pipe MRI (Phantom). The latter is the simplest test case.

## 1. Input files

### 1.1. Configuration files

To process a given MRI file, AngioTK needs configuration files tailored for this MRI. These files are used by the different pipeline modules and have the following default names:

```Filtering:
rorpo.cfg
Segmentation & extraction:
surfacefromimage.cfg
Centerlines definition:
centerlines.cfg
Centerline processing :
centerlinesmanager.cfg
Image reconstruction :
imagefromcenterlines.cfg
Surface extraction :
surfacefromimage2.cfg
Mesh reconstruction :
remeshstlgmsh.cfg
volumefromstlandcenterlines.cfg```

### 1.2. Centerline files

The centerline files are also needed, and should be placed in a subdirectory named `data`. See Using the centerlines editing graphical tool for further information.

 To allow the pipeline script to process the MRI, these files should all stay in the same directory (which path will be used as inputpath, see below)

## 2. Running AngioTK

AngioTK is launched using a python script with three paths as parameters:

• inputfile (where the MRI is)

• inputpath (where all the .cfg files are)

• outputpath (where the output should be written)

The whole command line used to process each MRI file as well as the needed corresponding configuration files path are detailed below.

Because users working environment may differ, we will use the following variables to refer to the needed paths. Please replace them accordingly.

• `INSTALL` refers to the path where AngioTK was installed (see the building page)

• `image.mha` is the original MRI.

• `OUTPUT` is where you wish to write results.

## 3. Examples

### 3.1. Example 1: Base1_000

`.cfg files path: $INSTALL/share/AngioTK/Examples/MeshFromMRI/` ``````python$INSTALL/bin/runAngioTKPipeline.py \
--inputfile image.mha \
--inputpath $INSTALL/share/AngioTK/Examples/MeshFromMRI/Base1_000/ \ --outputpath$OUTPUT``````

### 3.2. Example 2.a: Base2_FOA42 arterial

`.cfg files path: $INSTALL/share/AngioTK/Examples/MeshFromMRI/Base2_FOA42/artery` ``````python$INSTALL/bin/runAngioTKPipeline.py \
--inputfile image.mha \
--inputpath $INSTALL/share/AngioTK/Examples/MeshFromMRI/Base2_FOA42/artery/ \ --outputpath$OUTPUT``````

### 3.3. Example 2.b: Base2_FOA42 venous

`.cfg files path: $INSTALL/share/AngioTK/Examples/MeshFromMRI/Base2_FOA42/veinous` ``````python$INSTALL/bin/runAngioTKPipeline.py \
--inputfile image.mha \
--inputpath $INSTALL/share/AngioTK/Examples/MeshFromMRI/Base2_FOA42/veinous/ \ --outputpath$OUTPUT``````

### 3.4. Example 3.a: Base2_GEO26 arterial

`.cfg files path: $INSTALL/share/AngioTK/Examples/MeshFromMRI/Base2_GEO26/artery` ``````python$INSTALL/bin/runAngioTKPipeline.py \
--inputfile image.mha \
--inputpath $INSTALL/share/AngioTK/Examples/MeshFromMRI/Base2_GEO26/artery/ \ --outputpath$OUTPUT``````

### 3.5. Example 3.b: Base2_GEO26 venous

`.cfg files path: $INSTALL/share/AngioTK/Examples/MeshFromMRI/Base2_GEO26/veinous` ``````python$INSTALL/bin/runAngioTKPipeline.py \
--inputfile image.mha \
--inputpath $INSTALL/share/AngioTK/Examples/MeshFromMRI/Base2_GEO26/veinous/ \ --outputpath$OUTPUT``````

### 3.6. Example 4: Phantom (plastic tube)

`.cfg files path: $INSTALL/share/AngioTK/Examples/MeshFromMRI/Phantom` ``````python$INSTALL/bin/runAngioTKPipeline.py \
--inputfile image.mha \
--inputpath $INSTALL/share/AngioTK/Examples/MeshFromMRI/Phantom \ --outputpath$OUTPUT``````