FreeSurfer MRI Intensity Normalization¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Normalizes T1 image intensities so that white matter has a target intensity value (default 110).
Modality: T1-weighted 3D volume (MGZ format, within FreeSurfer pipeline).
Typical Use: Preparing T1 for segmentation within FreeSurfer pipeline.
Key Parameters¶
-n (number of iterations), -b (bias field smoothing sigma), -aseg (use aseg for normalization regions)
Key Points¶
Part of recon-all autorecon1. Creates nu.mgz (non-uniformity corrected) and T1.mgz (intensity normalized).
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
input |
File |
Yes | Input volume | |
output |
string |
Yes | Output normalized volume filename | |
gradient |
double |
No | Max intensity/mm gradient (default 1) | -g |
niters |
int |
No | Number of 3D normalization iterations | -n |
mask |
File |
No | Input mask file | -mask |
noskull |
boolean |
No | Do not normalize skull regions | -noskull |
aseg |
File |
No | Input segmentation for guidance | -aseg |
noaseg |
boolean |
No | Do not use aseg for normalization | -noaseg |
control_points |
File |
No | Control points file | -f |
seed |
int |
No | Random seed | -seed |
bias |
double |
No | Bias field FWHM | -b |
sigma |
double |
No | Sigma for bias field smoothing | -sigma |
brain_mask |
File |
No | Brain mask volume | -brainmask |
mprage |
boolean |
No | Assume darker gray matter (MPRAGE) | -mprage |
conform |
boolean |
No | Conform to 256^3 and 1mm | -conform |
gentle |
boolean |
No | Perform gentler normalization | -gentle |
disable_logging |
boolean |
No | Disable logging | -nolog |
Accepted Input Extensions¶
- input:
.mgz,.mgh,.nii,.nii.gz - mask:
.mgz,.mgh,.nii,.nii.gz - aseg:
.mgz,.mgh,.nii,.nii.gz - control_points:
.dat - brain_mask:
.mgz,.mgh,.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
normalized |
File |
$(inputs.output)* |
log |
File |
mri_normalize.log |
Output Extensions¶
- normalized:
.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