FreeSurfer Volume to Surface Projection¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Projects volumetric data (fMRI, PET, etc.) onto the cortical surface using specified sampling method.
Modality: 3D or 4D NIfTI/MGZ volume plus FreeSurfer subject registration.
Typical Use: Mapping functional or PET data to cortical surface for surface-based analysis.
Key Parameters¶
--mov (input volume), --reg (registration), --hemi (hemisphere), --projfrac (fraction of cortical thickness), --o (output)
Key Points¶
Use --projfrac 0.5 to sample at mid-cortical depth. Can average across depths with --projfrac-avg.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
source_file |
File |
Yes | Volume to sample from | --src |
hemi |
enum |
Yes | Hemisphere (lh or rh) | --hemi |
output |
string |
Yes | Output surface file | --out |
reg_file |
File |
No | Registration file (tkregister format) | --reg |
reg_header |
string |
No | Subject name for header registration | --regheader |
mni152reg |
boolean |
No | Use MNI152 registration | --mni152reg |
subject |
string |
No | Source subject name | --srcsubject |
trgsubject |
string |
No | Target subject (for resampling) | --trgsubject |
projfrac |
double |
No | Projection fraction along normal (0=white, 1=pial) | --projfrac |
projfrac_avg |
string |
No | Average along normal (start stop delta) | --projfrac-avg |
projfrac_max |
string |
No | Maximum along normal (start stop delta) | --projfrac-max |
projdist |
double |
No | Projection distance in mm | --projdist |
interp |
enum |
No | Interpolation method | --interp |
surf |
string |
No | Surface name (default white) | --surf |
surf_file |
File |
No | Explicit surface file | --surfval |
mask_label |
File |
No | Only sample within label | --mask |
cortex |
boolean |
No | Use cortex label as mask | --cortex |
frame |
int |
No | Only convert this frame | --frame |
out_type |
enum |
No | Output file format | --out_type |
Accepted Input Extensions¶
- source_file:
.mgz,.mgh,.nii,.nii.gz - reg_file:
.dat,.lta - surf_file:
.white,.pial,.inflated,.smoothwm,.orig - mask_label:
.label
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
out_file |
File |
$(inputs.output)* |
log |
File |
mri_vol2surf.log |
Output Extensions¶
- out_file:
.mgh,.mgz,.nii,.nii.gz,.w
Enum Options¶
interp: nearest, trilinear
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¶
- Functional MRI > FreeSurfer > Functional Analysis