Index

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>

mri_mask (last edited 2018-02-06 11:08:56 by BramDiamond)