Biology Reference
In-Depth Information
Fig. 7. Amira user interface for bone segmentation: (
a
) MicroCT image section of a mouse head, (
b
) bone surface visualization,
(
c
) segmentation tool interface, (
d
) manual tracing of occipital bone, (
e
) cleaning results by removing islands and holes.
Fig. 8. FreeSurfer segmentation results: different brain structures are painted with different colors.
(6) Run “Remove Islands” under the “Segmentation” menu to
remove small isolated noisy blobs (Fig.
7e
).
(7) Run “Save Data As” under the “File” menu to save the seg-
mentation results. For more complicated operations, see Amira
documentation:
http://www.amira.com/
.
The segmentation procedure described above is semiautomatic
and requires user intervention. Software tools are available that can
perform automatic segmentation. FreeSurfer (
15, 16
) (Table
3
) is
such an example that is widely used for whole brain segmentation
and cortical parcellation (Fig.
8
). It operates on good quality T1
weighted MRI scans, and instructions are available at
http://surfer.
Based on the segmentation results, one can directly perform
volumetric analysis of the segmented ROIs. Volumetric analysis is
Search WWH ::
Custom Search