FreeSurfer Surface to Sphere Mapping¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Maps the inflated cortical surface to a sphere for inter-subject spherical registration.
Modality: FreeSurfer inflated surface file.
Typical Use: Preparing cortical surface for spherical registration and atlas labeling.
Key Parameters¶
(minimal user-facing parameters; uses inflated surface)
Key Points¶
Prerequisite for cortical atlas registration. Part of recon-all. Spherical mapping enables vertex-wise inter-subject comparisons.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
input |
File |
Yes | Input inflated surface file | |
output |
string |
Yes | Output spherical surface filename | |
seed |
int |
No | Random number generator seed | -seed |
q |
boolean |
No | Omit self-intersection and vertex location info | -q |
p |
boolean |
No | Write intermediate surfaces | -p |
dist |
double |
No | Expand surface outward | -dist |
mval |
double |
No | Magic value for processing | -v |
in_smoothwm |
File |
No | Smooth white matter reference surface | -w |
niters |
int |
No | Number of iterations | -i |
dt |
double |
No | Time step for integration | -dt |
remove |
boolean |
No | Remove interseced faces | -remove |
Accepted Input Extensions¶
- input:
.inflated,.white,.pial,.smoothwm,.orig - in_smoothwm:
.smoothwm,.white,.pial,.orig
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
sphere |
File |
$(inputs.output)* |
log |
File |
mris_sphere.log |
Output Extensions¶
- sphere:
.sphere
Docker Tags¶
Available versions: latest, 8.1.0, 8.0.0, 7.2.0, 7.3.0, 7.3.1, 7.3.2, 7.4.1, 7.1.1, 6.0
Categories¶
- Structural MRI > FreeSurfer > Surface Reconstruction