FreeSurfer Cortical Atlas Labeling¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Applies a cortical parcellation atlas to an individual subject using trained classifier on spherical surface.
Modality: FreeSurfer subject directory with sphere.reg (requires completed recon-all).
Typical Use: Applying cortical parcellation atlas to individual subjects.
Key Parameters¶
Key Points¶
Uses Gaussian classifier atlas trained on manual labels. Part of recon-all. Different atlases available.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
subject |
string |
Yes | Subject name | |
hemi |
enum |
Yes | Hemisphere (lh or rh) | |
canonsurf |
File |
Yes | Canonical surface (e.g., sphere.reg) | |
classifier |
File |
Yes | Atlas classifier file (.gcs) | |
output |
string |
Yes | Output annotation filename | |
aseg |
File |
No | Aseg volume for additional context | -aseg |
l |
File |
No | Label file to restrict annotation | -l |
seed |
int |
No | Random seed | -seed |
t |
File |
No | Color table for output | -t |
orig |
string |
No | Original surface name | -orig |
sdir |
string |
No | Subjects directory | -sdir |
novar |
boolean |
No | Do not use variance in classification | -novar |
nbrs |
int |
No | Number of neighbors for classification | -nbrs |
Accepted Input Extensions¶
- canonsurf:
.sphere.reg,.sphere - classifier:
.gcs - aseg:
.mgz,.mgh,.nii,.nii.gz - l:
.label - t:
.txt,.ctab
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
annotation |
File |
$(inputs.output)* |
log |
File |
mris_ca_label.log |
Output Extensions¶
- annotation:
.annot
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 > Parcellation