| Here you can find the protocols that were used by Dr. Sowell's lab for processing brain images. Click the links below to view the protocol.
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Registration, Segmentation, and Masking
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Hemisphere Masking
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| Image registration reorients minc images from native
to reslice space. Segmentation classifies gray matter, white matter,
CSF, and background in the minc image. Masking cleans the image of non-brain tissues,
which then allows the whole brain to be modeled in 3D.
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Divide minc image into right and left hemispheres of the brain.
This allows for the medial surface of the brain to be created into a 3D model.
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Creating Lateral Objects
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Creating Medial Objects
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| A whole brain 3D model is created from a series of scripts. This model contains 65,000
points that can be used for statistical analyses.
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A hemisphere 3D model is created from a series of scritps. This model contains 65,000
points that can be used for statistical analyses.
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Surface Curve Drawing- Lateral
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Surface Curve Drawing- Medial
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| Sulcal lines are drawn on the lateral surface of the 3D model in order to define
homologous anatomy across subjects.
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Sulcal lines are drawn on the medial surface of the 3D model in order to define
homologous anatomy across subjects.
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305 space to Sulcal space
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Lateral Flatmapping
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| After the surface lines have been drawn, the subject's brain must be taken back into
its native space, and then to sulcal space in order for comparisons across subjects to be made.
This protocol details the steps that are needed to do this.
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The lateral surface must be flattened (made into a flatmap) and warped so that
statisical analyses on the data can be carried out.
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Medial Flatmapping
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| The medial surface must be flattened (made into a flatmap) and warped so that
statisical analyses on the data can be carried out.
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| Pipeline program
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| Pipeline is a program written by David Rex
that provides us with a graphical interface to perform various processes on data. More about the Pipeline
program can be found here
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General Pipeline notes
Leonard dataset Pipeline notes
Yale dataset Pipeline notes
Yale2 dataset Pipeline notes
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Cerebellum
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Creating Targets
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| This is the process in which the cerebellum is masked and modeled. This protocol has
not been finalized.
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This is a protocol that is a useful guide for creating the targets used in making
the 3D models.
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