spm_norm
Purpose:
Invoke the SPM spatial normalization program from the command line.ls
Usage:
spm_norm [-cn-m <matrix_file> -t <template> -s <voxel_size>] <filename>
Options:
- <filename>: The name of either an anatomical image or and EPI image.
- -t TEMPLATE, --template=TEMPLATE Template to be used.
- -m MATNAME, --mat_output_name=MATNAME File where transformation matrix should be stored.
- -c, --compute_only Compute transformation only.
- -n, --norm_only Normalize image file using precomputed transformation. This must be present if an EPI image is supplied. Otherwise the program will try to compute the normalization rather than just apply it.
Example
To compute the normalization:
spm_norm T1High.nii
This will normalize T1High to the MNI152 atlas with 2mm pixels in the spm5 distribution. The output will be written to wT1High.nii.
To apply the normalization:
spm_norm -nm T1High_sn.mat run_1_mf+orig
The EPI series will be converted to nifti format and spatially normalized. The output file would be wrun_1_mf.nii