FreeSurfer Segmentation Statistics¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Computes volume and intensity statistics for each region in a segmentation volume.
Modality: Segmentation volume (e.g., aseg.mgz) plus optional intensity volume.
Typical Use: Extracting regional volumes and mean intensities per structure.
Key Parameters¶
--seg (segmentation), --i (intensity volume), --ctab (color table), --sum (output summary file), --excludeid 0 (exclude background)
Key Points¶
Reports volume, mean intensity, and other statistics per region. Can use any segmentation volume.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
seg |
File |
Yes | Segmentation volume | --seg |
sum |
string |
Yes | Output summary file | --sum |
in |
File |
No | Input volume for intensity statistics | --in |
ctab |
File |
No | Color table file (e.g., FreeSurferColorLUT.txt) | --ctab |
ctab_default |
boolean |
No | Use default FreeSurfer color table | --ctab-default |
annot |
string |
No | Annotation (subject hemi parc) | --annot |
slabel |
string |
No | Surface label (subject hemi label) | --slabel |
id |
int[] |
No | Only report these segmentation IDs | --id |
excludeid |
int |
No | Exclude this segmentation ID (usually 0) | --excludeid |
excl_ctxgmwm |
boolean |
No | Exclude cortex GM and WM | --excl-ctxgmwm |
nonempty |
boolean |
No | Only report non-empty segmentations | --nonempty |
mask |
File |
No | Mask volume | --mask |
maskthresh |
double |
No | Mask threshold | --maskthresh |
maskinvert |
boolean |
No | Invert mask | --maskinvert |
subject |
string |
No | Subject name | --subject |
avgwf |
string |
No | Output average waveform file | --avgwf |
avgwfvol |
string |
No | Output average waveform as volume | --avgwfvol |
sfavg |
string |
No | Spatial-frame average file | --sfavg |
brain_vol_from_seg |
boolean |
No | Compute brain volume from segmentation | --brain-vol-from-seg |
brainmask |
File |
No | Brain mask file | --brainmask |
pv |
File |
No | Partial volume file | --pv |
robust |
double |
No | Compute robust statistics (percent) | --robust |
euler |
boolean |
No | Report Euler number | --euler |
Accepted Input Extensions¶
- seg:
.mgz,.mgh,.nii,.nii.gz - in:
.mgz,.mgh,.nii,.nii.gz - ctab:
.txt,.ctab - mask:
.mgz,.mgh,.nii,.nii.gz - brainmask:
.mgz,.mgh,.nii,.nii.gz - pv:
.mgz,.mgh,.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
summary |
File |
$(inputs.sum) |
avgwf_file |
File |
$(inputs.avgwf) |
avgwfvol_file |
File |
$(inputs.avgwfvol) |
log |
File |
mri_segstats.log |
Output Extensions¶
- summary:
.stats,.txt,.dat,.csv - avgwf_file:
.txt,.dat - avgwfvol_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¶
- Structural MRI > FreeSurfer > Morphometry