FreeSurfer Cortical Parcellation to Volume¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Combines surface-based cortical parcellation (aparc) with volumetric subcortical segmentation (aseg) into a single volume.
Modality: FreeSurfer subject directory (requires completed recon-all).
Typical Use: Creating volumetric parcellation from surface labels for ROI analysis.
Key Parameters¶
--s (subject), --annot (annotation name, default aparc), --o (output volume)
Key Points¶
Creates aparc+aseg.mgz combining ~80 cortical and subcortical regions. Different parcellation schemes 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 | --s |
output |
string |
No | Output volume filename | --o |
volmask |
File |
No | Volume mask for output | --volmask |
annot |
string |
No | Parcellation name (default aparc) | --annot |
a2005s |
boolean |
No | Use aparc.a2005s parcellation | --a2005s |
a2009s |
boolean |
No | Use aparc.a2009s parcellation | --a2009s |
labelwm |
boolean |
No | Also label white matter parcels | --labelwm |
rip_unknown |
boolean |
No | Rip unknown label | --rip-unknown |
hypo_as_wm |
boolean |
No | Label hypointensities as white matter | --hypo-as-wm |
noribbon |
boolean |
No | Do not use ribbon constraint | --noribbon |
ribbon |
File |
No | Use specified ribbon file | --ribbon |
ctxseg |
boolean |
No | Create segmentation of cortex | --ctxseg |
wmparc_dmax |
double |
No | Distance max for WM parcellation | --wmparc-dmax |
ctxgmrmax |
double |
No | Radius for cortical GM assignment | --crs-test |
Accepted Input Extensions¶
- volmask:
.mgz,.mgh,.nii,.nii.gz - ribbon:
.mgz,.mgh,.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
aparc_aseg |
File |
$(inputs.output), *aparc+aseg*.mgz, *aparc+aseg*.nii.gz |
log |
File |
mri_aparc2aseg.log |
Output Extensions¶
- aparc_aseg:
.mgz,.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