mri_long_normalize
mri__long_normalize <input vol> <base-tp file> <output vol>
Normalize the white-matter, optionally based on control points. The input volume is converted into a new volume where white matter image values all range around 110.
| Argument | Explanation |
|---|---|
| <input vol> | input mri volume file |
| <output vol> | output mri volume file |
| Argument | Explanation |
|---|---|
| -n <int n> | use n 3d normalization iterations (default=2) |
| -no1d | disable 1d normalization |
| -sigma sigma | smooth bias field |
| -a aseg | |
| -v Gvx Gvy Gvz | for debugging |
| -d Gx Gy Gz | for debugging |
| -r controlpoints biasfield | for reading |
| -u or -h | print usage |
mri_normalize SUBJECT/mri/nu.mgz SUBJECT/mri/T1.mgz
Uses the nu volume (nonuniformity corrected volume), and creates the T1 volume, with white matter voxels around 110 image value
mri_long_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz $SUBJECTS_DIR/bert_base/base-tps brain.mgz
Uses the norm volume, and creates the brain volume, making use of the aseg and masking with brainmask
\"Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction\", Dale, A.M., Fischl, B., Sereno, M.I. (1999) NeuroImage 9(2):179-194
Report bugs to <freesurfer@nmr.mgh.harvard.edu>
nu_correct, mri_fill