mri_nu_correct.mni
*********************************************
Wrapper for nu_correct, a program from the Montreal Neurological Insitute (MNI) used for correcting intensity non-uniformity (ie, bias fields). You must have the MNI software installed on your system to run this. See www.bic.mni.mcgill.ca/software/N3 for more info.
| Argument | Explanation |
|---|---|
| --i invol | input volume. Input can be any format accepted by mri_convert. |
| --o outvol | output volume. Output can be any format accepted by mri_convert. If the output format is COR, then the directory must exist. |
| --n niters | Number of iterations to run nu_correct. Default is 4. This is the number of times that nu_correct is repeated (ie, using the output from the previous run as the input for the next). This is different than the -iterations option to nu_correct. |
| --proto-iters Np | Passes Np as argument of the -iterations flag of nu_correct. This is different than the --n flag above. Default is not to pass nu_correct the -iterations flag. |
| --stop thresh | Passes thresh as argument of the -stop flag of nu_correct. According to the nu_correct documentation, this threshold is the \"CV of change in field estimate below which iteration stops (suggest 0.01 to 0.0001)\". Default is not to pass nu_correct the -stop flag. |
| --uchar tal.xfm | Use mri_make_uchar instead of conforming |
| --no-uchar | Do not use mri_make_uchar (default) |
| --cm | For use with data that is higher than 1mm resolution. |
| Argument | Explanation |
|---|---|
| --help | print help and exit |
| --debug | turn on debugging |
| --version | print version and exit |
Report bugs to <freesurfer@nmr.mgh.harvard.edu>