mri_mask - applies a mask volume ( typically skull stripped )
mri_mask [options] <in vol> <mask vol> <out vol>
This program applies a mask volume ( typically skull stripped ).
| Argument | Explanation |
|---|---|
| in vol | input volume |
| mask vol | mask volume |
| Argument | Explanation |
|---|---|
| -xform %s | apply LTA transform to align mask to input volume |
| -invert | reversely apply -xform |
| -lta_src %s | source volume for -xform (if not available from the xform file) |
| -lta_dst %s | target volume for -xform (if not available from the xform file) |
| -T threshold | threshold mask volume at threshold (i.e., all values <= T considered as zero) |
| -bb npad | Create and extract data from a bounding box around the mask. The bounding box is expanded by npad voxels in each direction. npad should be at least 1 to avoid clipping |
| -abs | take abs() before applying threshold |
| -transfer # | transfer only voxel value # from mask to out |
| -keep_mask_deletion_edits | transfer voxel-deletion edits (voxels=1) from mask to out vol |
| Output | Explanation |
|---|---|
| out vol | output volume |
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>