PIPELINE IMAGE PROCESSING

Data collection
Patients who were treated with RT for

1 pituitary tumor. Criteria inclusion:

treatment planning CT with dose map and
PTV and MRI before and at leat a follow-up
MRI beetween 60-360 days after RT.

Registration
Crop non-brain tissue from a CT image with
2 the associated PTV maps. Register to the T1
MR images using tools like 3D Slicer and ANTs
(Advanced Normalization Tools).

Preprocessing

3 Register the cropped CT image with the

corresponding PTV maps to the T1 MR
images.

Cortical Thickness Estimation

4
We performed segmentation using FastSufer
version 6.0 and we use FreeSurfer to get the
cortical parcellation following the Desikan-
Killiany-Tourville Atlas.

Differences in cortical thickness

5 Calculate by substracting the baseline and

the follow-up cortical thickness surfaces in
every vertex.

Relation beetween dose and thickness

change

6 Map the PTV and dose to the surface,

censoring the region linked to the PTV, and
find the correlation between dose and
thickness changes.

IMAGE PRE PROCESSING AND

SEGMENTATION
Data Brain PTV region Image
collection masking Labeling registration

MRI CT

Convert DICOM data to Remove non-brain tissue Load CT NIfTI data into 3D Slicer Align of the PTV region and
NIIFTI format and to from a CT image. and extract PTV information to T1w data in the same spatial
anonimize it. generate a binary label map for coordinate system to
this region." generate a new image.
Python routines FSL - BET
3D Slicer 3D Slicer - ANTs rigid registration

Crop Remove Differences in

Segmentation
volume PTV cortical thickness

Select an axial image for PTV
labeling and generate a 3D
model for visualization.
3D Slicer - Segment Editor and Grow
Cut Segmentation
Set the value to '0' within the
PTV region and generate a
new NIfTI image with the PTV
region excluded.
3D Slicer - Volume Clip module
Load the new Nii image and to
run the automate
segmentation of whole brain
structures.
Freesurfer - Recon-all
Subtracting cortical
thickness from T1W images
pre- and post-radiotherapy
treatment.
3D Slicer - Freesurfer