FreeSurfer MRI White Matter Segmentation¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Segments white matter from normalized T1 image using intensity thresholding and morphological operations.
Modality: Intensity-normalized T1 volume (T1.mgz from mri_normalize).
Typical Use: White matter identification for surface reconstruction.
Key Parameters¶
-thicken (thicken WM), -wlo/-whi (WM intensity range)
Key Points¶
Part of recon-all. Outputs wm.mgz used for surface reconstruction. Quality depends on good intensity normalization.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
input |
File |
Yes | Input normalized volume (white matter ~110) | |
output |
string |
Yes | Output segmentation filename | |
wlo |
double |
No | White matter low intensity threshold | -wlo |
whi |
double |
No | White matter high intensity threshold | -whi |
glo |
double |
No | Gray matter low intensity threshold | -glo |
ghi |
double |
No | Gray matter high intensity threshold | -ghi |
thicken |
int |
No | Thicken option (0 to disable) | -thicken |
nseg |
int |
No | Number of segmentation classes | -nseg |
mprage |
boolean |
No | Assume MPRAGE contrast (darker gray matter) | -mprage |
slope |
double |
No | Slope for threshold adjustment | -slope |
nmin |
int |
No | Minimum number of white matter voxels | -nmin |
keep |
boolean |
No | Keep intermediate files | -keep |
Accepted Input Extensions¶
- input:
.mgz,.mgh,.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
segmentation |
File |
$(inputs.output)* |
log |
File |
mri_segment.log |
Output Extensions¶
- segmentation:
.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 > Surface Reconstruction