FreeSurfer Surface to Volume Projection¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Projects surface-based data back to volumetric space using registration and template volume.
Modality: FreeSurfer surface overlay file plus template volume and registration.
Typical Use: Converting surface-based results back to volume space for reporting.
Key Parameters¶
--surfval (surface data), --reg (registration), --template (output grid template), --hemi (hemisphere), --o (output volume)
Key Points¶
Inverse of mri_vol2surf. Template defines output grid dimensions.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
source_file |
File |
Yes | Surface values file | --surfval |
hemi |
enum |
Yes | Hemisphere (lh or rh) | --hemi |
output |
string |
Yes | Output volume filename | --o |
reg |
File |
No | Registration file | --reg |
identity |
string |
No | Subject for identity registration | --identity |
template |
File |
No | Template volume for output geometry | --template |
subject |
string |
No | Subject name | --subject |
surf |
string |
No | Surface name (default white) | --surf |
mkmask |
boolean |
No | Create mask volume | --mkmask |
projfrac |
double |
No | Projection fraction along normal | --projfrac |
projdist |
string |
No | Projection distances (min max delta) | --projdist |
fill_projfrac |
string |
No | Fill between projection fractions (start stop delta) | --fill-projfrac |
fillribbon |
boolean |
No | Fill entire cortical ribbon | --fillribbon |
ribbon |
File |
No | Ribbon volume file | --ribbon |
merge |
File |
No | Merge with existing volume | --merge |
add |
boolean |
No | Add to merged volume | --add |
vtxvol |
boolean |
No | Create vertex volume | --vtxvol |
Accepted Input Extensions¶
- source_file:
.mgh,.mgz,.nii,.nii.gz,.w,.curv,.sulc,.thickness,.area - reg:
.dat,.lta - template:
.mgz,.mgh,.nii,.nii.gz - ribbon:
.mgz,.mgh,.nii,.nii.gz - merge:
.mgz,.mgh,.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
out_file |
File |
$(inputs.output)* |
log |
File |
mri_surf2vol.log |
Output Extensions¶
- out_file:
.mgz,.mgh,.nii,.nii.gz
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