FreeSurfer Label to Volume Conversion¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Converts surface-based labels to volumetric ROIs using a registration matrix.
Modality: FreeSurfer label file plus template volume and registration.
Typical Use: Creating volumetric ROIs from FreeSurfer surface parcellations.
Key Parameters¶
--label (input label), --temp (template volume), --reg (registration file), --o (output volume), --proj (projection parameters)
Key Points¶
Requires registration between surface and target volume space. Use --proj to control projection depth.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
label |
File |
No | Label file to convert | --label |
annot |
File |
No | Annotation file to convert | --annot |
seg |
File |
No | Segmentation file to convert | --seg |
temp |
File |
Yes | Template volume for output geometry | --temp |
output |
string |
Yes | Output volume filename | --o |
reg |
File |
No | Registration file (source to anat) | --reg |
identity |
boolean |
No | Use identity matrix for registration | --identity |
subject |
string |
No | Subject name for surface labels | --subject |
hemi |
enum |
No | Hemisphere for surface labels | --hemi |
proj |
string |
No | Projection method and parameters (frac/abs start stop delta) | --proj |
fill_thresh |
double |
No | Fill threshold (0-1) | --fillthresh |
label_voxel_volume |
boolean |
No | Fill with voxel volume instead of 1 | --label-voxel-volume |
native_vox2ras |
boolean |
No | Use native vox2ras | --native-vox2ras |
surf |
string |
No | Surface name for projection (default white) | --surf |
hits |
string |
No | Save hits volume | --hits |
labvoxvol |
boolean |
No | Label with voxel volume | --labvoxvol |
Accepted Input Extensions¶
- label:
.label - annot:
.annot - seg:
.mgz,.mgh,.nii,.nii.gz - temp:
.mgz,.mgh,.nii,.nii.gz - reg:
.dat,.lta
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
label_volume |
File |
$(inputs.output)* |
hits_volume |
File |
$(inputs.hits) |
log |
File |
mri_label2vol.log |
Output Extensions¶
- label_volume:
.mgz,.mgh,.nii,.nii.gz - hits_volume:
.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¶
- Structural MRI > FreeSurfer > Parcellation