Deletions are marked like this. | Additions are marked like this. |
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|| ?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 || || |
|| ?h.pial || mris_fill -c -r 1 || ?h.pial.filled.mgz || || <1min || || ?h.pial.filled.mgz || make_outer_surface -se 15 || ?h.pial-outer || matlab commands, morphological closing*|| <2min || || ?h.pial-outer || mris_smooth -nw -n 3 || ?h.pial-outer-smoothed || || <1min|| || ?h.pial, ?h.pial-outer-smoothed || make_roi_paths || ?h.pial.*.path, ?h.pial.*.center || matlab commands || || || ?h.pial.*.path, ?h.pial.*.center || make_roi_labels || ?h.pial.*.label || wrapper for mri_path2label || || || ?h.pial, ?h.pial-outer-smoothed || mris_compute_lgi || ?h.lgi.mgh || matlab command || || |
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For each region of interest on the outer surface (ROIo), a corresponding region of interest is obtained on the pial surface (referred as ROIp in the validation paper). The correspondance is based on both the proximity with the ROIo's perimeter and geodesical constraints. | For each region of interest on the outer surface (ROIo), a corresponding region of interest is obtained on the pial surface (referred as ROIp in the validation paper). The correspondance is based on both the proximity with the ROIo's perimeter and geodesical constraints. |
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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 Overview
Input |
Process |
Output |
Notes |
Computation time |
?h.pial |
mris_fill -c -r 1 |
?h.pial.filled.mgz |
|
<1min |
?h.pial.filled.mgz |
make_outer_surface -se 15 |
?h.pial-outer |
matlab commands, morphological closing* |
<2min |
?h.pial-outer |
mris_smooth -nw -n 3 |
?h.pial-outer-smoothed |
|
<1min |
?h.pial, ?h.pial-outer-smoothed |
make_roi_paths |
?h.pial.*.path, ?h.pial.*.center |
matlab commands |
|
?h.pial.*.path, ?h.pial.*.center |
make_roi_labels |
?h.pial.*.label |
wrapper for mri_path2label |
|
?h.pial, ?h.pial-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
1. 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 |
2. Computation of the regions of interest on the outer surface in matlab (CURRENTLY: ~2h FOR AN OUTER MESH OF ~80'000 VERTICES)
For each one on 100 vertex of the outer surface (that we denote iV), 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 |
including reorganization of the vertices' list in the right order |
|
save a seed point at the center of the future pial region of interest for subsequent propagation |
?h.c_* |
seed points are defined as the vertex of the pial surface which is closest to the iV on the outer surface (currently < 2min) |
3. Computation of the regions of interest on the outer surface using FreeSurfer
For each region of interest on the outer surface (ROIo), a corresponding region of interest is obtained on the pial surface (referred as ROIp in the validation paper). The correspondance is based on both the proximity with the ROIo's perimeter and geodesical constraints.
Input |
Process |
Output |
Notes |
?h.*.path |
mri_path2label --fill SUBJID ?h centerSeed --i ?h.*.path --o ./?h.ROIp_*.label |
?h.ROIp_*.label |
to compute iteratively for each iV |
4. Computation of the lGI measurements and creation of cortical gyrification maps in matlab
Input |
Process |
Output |
Notes |
?h.ROIp_*.label |
area measurement, lGI ratio computation |
?h.lGI_outer.mat |
lGI values sampled on the outer surface |
?h.lGI_outer.mat |
propagation to the pial surface |
?h.lGI_pial.mgh |
lGI values are weighted according to their prior involvement in the whole computational process with weighting inversely proportional to the distance to the outer surface's normal |