Index
Contents
Name
mri_mask - This program applies a mask volume ( typically skull stripped )
Synopsis
mri_mask [options] <in vol> <mask vol> <out vol>
Arguments
Positional Arguments
in vol |
input volume |
mask vol |
mask volume |
Required Flagged Arguments
Optional Flagged Arguments
-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 mask volume at # (i.e., all values <= T is 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 |
Outputs
out vol |
output volume |
Description
Examples
Example 1
mri_mask -transfer 255 -keep_mask_deletion_edits wm.mgz <path_to_old_dir>/subject/mri/wm.mgz wm.mgz
Transfers white matter edits from a wm.mgz volume created with an older version of FreeSurfer to a wm.mgz created with a more recent version of FreeSurfer. The command should be run from <path_to_new_dir>/subject/mri/, i.e. where the newer copy of the wm.mgz volume resides.
Example 2
description
Bugs
None
See Also
Links
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>