Connectome Workbench CIFTI Smoothing¶
Library: Connectome Workbench | Docker Image: khanlab/connectome-workbench
Function¶
Applies geodesic Gaussian smoothing to CIFTI data on cortical surfaces and Euclidean smoothing in subcortical volumes.
Modality: CIFTI dense file plus surface files for each hemisphere.
Typical Use: Spatial smoothing of fMRI data in CIFTI format for HCP-style pipelines.
Key Parameters¶
Key Points¶
Surface smoothing follows cortical geometry (geodesic). Typical kernel 4-6mm FWHM. -fix-zeros prevents smoothing across medial wall.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
cifti_in |
File |
Yes | Input CIFTI file | |
surface_kernel |
double |
Yes | Gaussian surface smoothing kernel size in mm (sigma unless -fwhm) | |
volume_kernel |
double |
Yes | Gaussian volume smoothing kernel size in mm (sigma unless -fwhm) | |
direction |
enum |
Yes | Smoothing dimension (ROW or COLUMN) | |
cifti_out |
string |
Yes | Output smoothed CIFTI file | |
fwhm |
boolean |
No | Interpret kernel sizes as FWHM instead of sigma | -fwhm |
left_surface |
File |
No | Left cortical surface file | -left-surface |
right_surface |
File |
No | Right cortical surface file | -right-surface |
cerebellum_surface |
File |
No | Cerebellum surface file | -cerebellum-surface |
fix_zeros_volume |
boolean |
No | Treat volume zeros as missing data | -fix-zeros-volume |
fix_zeros_surface |
boolean |
No | Treat surface zeros as missing data | -fix-zeros-surface |
merged_volume |
boolean |
No | Smooth across subcortical structure boundaries | -merged-volume |
cifti_roi |
File |
No | CIFTI ROI to restrict smoothing | -cifti-roi |
Accepted Input Extensions¶
- cifti_in:
.dtseries.nii,.dscalar.nii,.dlabel.nii,.dconn.nii - left_surface:
.surf.gii - right_surface:
.surf.gii - cerebellum_surface:
.surf.gii - cifti_roi:
.dscalar.nii,.dlabel.nii,.dtseries.nii,.dconn.nii
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
smoothed_cifti |
File |
$(inputs.cifti_out) |
log |
File |
wb_cifti_smoothing.log |
err_log |
File |
wb_cifti_smoothing.err.log |
Output Extensions¶
- smoothed_cifti:
.dtseries.nii,.dscalar.nii
Docker Tags¶
Available versions: latest
Categories¶
- Functional MRI > Connectome Workbench > Surface Smoothing