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Intermediate steps in mris_compute_lgi (all matlab) are as follow: |
=== Detailed Stages' Description === ==== Creation of the mesh structure in matlab ==== |
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==== Computation of the regions of interest on the outer surface ==== For each one on 100 vertex of the outer surface, a circular region of interest is defined (referred as ROIo in the validation paper). The area of this region will become the above term of the lGI ratio computation at that vertex. || '''Input''' || '''Process''' || '''Output''' || '''Notes''' || || ?h.outer-smoothed-mesh || definition of the circular region of interest || || (based on intersection with a sphere with a geodesical constraint) || || || measurement of its area || ?h.outerROIareas.mat || || || || transfer of the points on the pial surface || ?h.path_*.path || (including reorganization of the vertices' list in the right order)) || |
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
- 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).
- 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, morphological closing* |
<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!)
Detailed Stages' Description
Creation of the mesh structure in matlab
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 |
computeNormals |
?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 |
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: 5 min for h=2 ; 15min for h=3; x min for h=4 |
Computation of the regions of interest on the outer surface
For each one on 100 vertex of the outer surface, a circular region of interest is defined (referred as ROIo in the validation paper). The area of this region will become the above term of the lGI ratio computation at that vertex.
Input |
Process |
Output |
Notes |
?h.outer-smoothed-mesh |
definition of the circular region of interest |
|
(based on intersection with a sphere with a geodesical constraint) |
|
measurement of its area |
?h.outerROIareas.mat |
|
|
transfer of the points on the pial surface |
?h.path_*.path |
(including reorganization of the vertices' list in the right order)) |