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'''Index'''
<<TableOfContents>>


= 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 =
FreeSurfer

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>