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 1. From a freesurfer surface file (primarily ?h.pial, but ?.white or other surface files are possible), an 'outer surface' surface file is created, called ?h.outer-pial, which is basically an 'enveloped', version of the (pial) input. It is created by a morphological closing operation which operates on a volume created using mris_fill (taking as input the pial surface file), using a sphere as the structural element (se).    1. From a freesurfer surface file (primarily ?h.pial, but ?.white or other surface files are possible), an 'outer surface' surface file is created, called ?h.outer-pial, which is basically an 'enveloped', version of the (pial) input. It is created by a morphological closing operation which operates on a volume created using mris_fill (taking as input the pial surface file), using a sphere as the structural element (se).
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* decreasing the diameter of the se sphere below 10mm will produce an outer surface entering in the sulci, increasing it do not substantially affect eh morphology of the outer surfaces (but increase computation time!)  * decreasing the diameter of the se sphere below 10mm will produce an outer surface entering in the sulci, increasing it do not substantially affect the morphology of the outer surfaces (but increase computation time!)
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Intermediate steps in mris_compute_lgi (all matlab) are as follow:
|| '''Input''' || '''Process''' || '''Output''' || '''Computation time''' ||
|| ?h.pial || createMeshFacesOfVertex || ?h.pial-mesh: mesh structure consisting of faces, vertices, and FacesOfVertex (backward info) || || 2min ||
|| ?h.outer-smoothed || createMeshFacesOfVertex || ?h.outer-smoothed-mesh: mesh structure consisting of faces, vertices, and faces' normal vector || || 20-25min ||
|| ?h.outer-smoothed-mesh || createMeshFacesOfVertex || ?h.outer-smoothed mesh structure consisting of faces, vertices, faces' normal and FacesOfVertex (backward info) || || 2min ||
|| ?h.outer-smoothed-mesh || averagingNormals -horizon h || ?h.outer-smoothed mesh structure consisting of faces, vertices, faces'normal, FacesOfVertex, and an average normal per vertex computed as a function of neighboorhood || || depending on the horizon: for h=2: 5 min; for h=3: 15min; for h=4: ||


Local Gyrification Index (LGI)

Overview

Gyrification index is a metric that quantifies the amount of cortex buried within the sulcal folds as compared with the amount of cortex on the outer visible cortex. A cortex with extensive folding has a large gyrification index, whereas a cortex with limited folding has a small gyrification index. The method to be incorporated into Freesurfer is based on that of Marie Schaer, [http://ltswww.epfl.ch/~schaer/Schaer_TMI_accepted.pdf "A Surface-based Approach to Quantify Local Cortical Gyrification"], which computes local measurements of gyrification at thousands of points over the whole cortical surface.

Processing Stream

Stages

  1. From a freesurfer surface file (primarily ?h.pial, but ?.white or other surface files are possible), an 'outer surface' surface file is created, called ?h.outer-pial, which is basically an 'enveloped', version of the (pial) input. It is created by a morphological closing operation which operates on a volume created using mris_fill (taking as input the pial surface file), using a sphere as the structural element (se).
  2. Once the outer-surface file is available, then the local gyrification measurements are calculated for each vertex of the outer-surface. To do this, circular regions of interest are defined for each vertex on the outer-surface, and the corresponding areas of each ROI are found on the pial surface. Finally, the local gyrification index (lGI) values are calculated at each pial vertices, and a scalar file is output (used in a similar manner as a 'thickness' scalar file).

I/O

Input

Process

Output

Notes

Computation time

?h.pial

mris_fill -c -r 1

?h.pial.mgz

<1min

?h.pial.mgz

make_outer_surface -se 15

?h.outer-pial

matlab command *

<2min

?h.outer-pial

mris_smooth -nw -n 3

?h.outer-smoothed

<1min

?h.outer-smoothed

mris_compute_lgi

?h.lgi.mgh

matlab command

* decreasing the diameter of the se sphere below 10mm will produce an outer surface entering in the sulci, increasing it do not substantially affect the morphology of the outer surfaces (but increase computation time!)

Intermediate steps in mris_compute_lgi (all matlab) are as follow:

Input

Process

Output

Computation time

?h.pial

createMeshFacesOfVertex

?h.pial-mesh: mesh structure consisting of faces, vertices, and FacesOfVertex (backward info)

2min

?h.outer-smoothed

createMeshFacesOfVertex

?h.outer-smoothed-mesh: mesh structure consisting of faces, vertices, and faces' normal vector

20-25min

?h.outer-smoothed-mesh

createMeshFacesOfVertex

?h.outer-smoothed mesh structure consisting of faces, vertices, faces' normal and FacesOfVertex (backward info)

2min

?h.outer-smoothed-mesh

averagingNormals -horizon h

?h.outer-smoothed mesh structure consisting of faces, vertices, faces'normal, FacesOfVertex, and an average normal per vertex computed as a function of neighboorhood

depending on the horizon: for h=2: 5 min; for h=3: 15min; for h=4:

LGI (last edited 2015-09-18 17:22:55 by LeeTirrell)