Manual segmentation protocol
Selected scans were chosen from two sets of images of premature infants scanned at term equivalent age, and one set of images of preterm infants scanned at a gestational age around 30 weeks. No brain pathology was visible on MRI, additional 15 months follow-up corrected for gestational age was normal according to Griffith’s assessment test. All scans were acquired on a Philips 3T system as follows:
- Axial scans acquired at 40 weeks corrected age
- Axial 3DT1-weighted: TR=9.4 ms; TE=4.6 ms; scan time=3.44 min, FOV=180×180; reconstruction matrix=512×512; consecutive sections with thickness=2.0 mm; number of sections=50, in-plane resolution 0.35 mm x 0.35 mm;
- Axial T2-weighted images: TR=6293 ms; TE=120 ms; scan time=5.40 min; FOV=180×180; reconstruction matrix=512×512; consecutive sections with thickness=2.0 mm; number of sections=50, in-plane resolution 0.35 mm x 0.35 mm
- Coronal scans acquired at 30 weeks corrected age
- Coronal 3DT1-weighted: TR=9.4 ms; TE=4.6 ms; scan time=4.44 min, FOV=130×100; reconstruction matrix=384×384; consecutive sections with thickness=2.0 mm; number of sections=50, in-plane resolution 0.34 mm x 0.34 mm;
- Coronal T2-weighted images: TR=10085 ms; TE=120 ms; scan time=6.23 min; FOV=130×100; reconstruction matrix=384×384; consecutive sections with thickness=2.0 mm; number of sections=50, in-plane resolution 0.34 mm x 0.34 mm
- Coronal scans acquired 40 weeks corrected age
- Coronal 3DT1-weighted: TR=9.5 ms; TE=4.6 ms; scan time=7.02 min, FOV=200×200; reconstruction matrix=256×256; consecutive sections with thickness=1.2 mm; number of sections=110, in-plane resolution 0.78 mm x 0.78 mm;
- Coronal T2-weighted images: TR=4847 ms; TE=150 ms; scan time=5.05 min; FOV=180×180; reconstruction matrix=512×512; consecutive sections with thickness=1.2 mm; number of sections=110, in-plane resolution 0.35 mm x 0.35 mm
Images for the NeoBrainS12 were obtained from the scanner without any post-processing. Dicom format was transformed to mhd+raw data.
The following tissues classes were segmented: cortical grey matter (CoGM), unmyelinated white matter (UWM), brainstem, cerebellum, ventricles, cerebrospinal fluid in the extracerebral space (CSF), basal ganglia and thalami, myelinated white matter (MWM).
Each tissue class was segmented separately. Manual (reference) segmentations have been defined on T2-weighted images. They were generated using an in-house developed user interface by mouse painting of brain voxels in all slices. Each voxel was assigned to only one of the eight tissue classes. The labeling was indicated by color overlay where each tissue class was represented by one color. During manual segmentation, observers were free to adjust window and level settings and use zoom-in and zoom-out functions.
When segmenting CoGM, UWM and CSF, the outer border of each tissue was carefully identified, while the inner border was over-segmented. For example, when segmenting CoGM, the outer border was carefully identified along the CSF border, while CoGM was over-segmented on the inner border (with UWM). When segmenting UWM, its outer border, thus the voxels touching CoGM were carefully identified. Thereafter, final segmentation of CoGM was achieved by subtracting voxels identified as UWM from those defined as CoGM. Similarly, CSF was finally defined by subtracting segmentation of CoGM from it. The inner border of UWM was defined by basal ganglia or ventricles or MWM. Therefore, its final segmentation was obtained by subtracting manual segmentation of ventricles, basal ganglia and MWM from its initial manual segmentation.
After all tissues classes had been segmented, the individual segmentations were added to form a total brain segmentation. This image was formed to make sure all voxels were assigned to a single tissue type and no unassigned brain voxels remained. Manual segmentations were corrected accordingly, if needed.
The segmentations were performed as follows:
- Cortical grey matter: CoGM could be very well distinguished from surrounding tissue as CSF and UWM by its lower intensity. Where the sulci touched each other, this was defined as a continuum. When CSF (higher signal) was seen in between sulci, this was defined as such.
- Unmyelinated white matter: The outer border ofUWM could be well distinguished from CoGM by its higher intensity. The subplate region and migrating bands were included in UWM (especially in the 30 week set).
- Brainstem: The borders of the brainstem with the cerebellum were clearly visible on the T2-weighted images. To clearly identify the border between basal ganglia and cerebellum, the overview plane (zoom-out) was used. The peduncles were included in the brainstem when they were not myelinated. When myelination was present, that part of the peduncles was included in the myelinated white matter (please see below).
- Cerebellum was defined by including the vermis until the peduncles started.
- Ventricles: Lateral ventricles and third and fourth ventricles were defined by utilizing the clear intensity difference between ventricles and the surrounding brain tissue.
- CSF: All CSF not included in the definition of the ventricles was defined as CSF. This also included the cavum septum pellucidum and the CSF around the brainstem.
- Basal ganglia and thalami: The borders to the white matter were easy to distinguish based on signal intensity. The border to the brainstem was defined as described before. The germinal matrix is a very small zone, and it was not segmented separately but included in the basal ganglia/thalamus class. When myelination was present, that part was included in the myelinated white matter, especially the PLIC.
- Myelinated white matter: When labeling myelinated white matter both T1- and T2-weighted images were inspected. MWM was defined as an area of lower signal intensity compared to the basal ganglia/white matter on the T2-weighted scan, in combination with an higher signal intensity on the T1-weighted scan. As an additional check, intensity based thresholding was used to identify areas of higher signal on the T1-weighted image automatically, and to check whether these areas were included in the MWM segmentation of the T2-weighted image. MWM included the peduncles, brainstem, basal ganglia/thalamus, and in some patients cortical spinal tracts could be followed into the white matter. The optical tract was not included.
Large vessels (>2-3mm) such as basil artery or large sinuses, were not classified as such but were defined as background. Small vessels were included in the tissue where they were situated.
The segmentations were performed either by MDs who were working towards a PhD in neonatology, or by trained medical students. The segmentations were verified independently by three neonatologists with each at least seven years of experience in reading neonatal MRI scans. In case of disagreement, the decision on the segmentation was made in a consensus meeting.
Images of two patients scanned axially at 40 weeks corrected age and images of two patients scanned coronally acquired at 30 weeks corrected age are available for training. For each set T1-weighted and T2-weighted images as well as the corresponding reference segmentations are available.
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