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)
-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

Links

FreeSurfer

Reporting Bugs

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

-Deletions are marked like this.
+Additions are marked like this.
 Line 22:
-|| in vol || input volume || ||

|| mask vol || mask volume || ||
+|| in vol || input volume ||

|| mask vol || mask volume ||
 Line 28:
-|| -xform %s || apply LTA transform to align mask to input volume || ||
+|| -xform %s || apply LTA transform to align mask to input volume ||
 Line 30:
-|| 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) || ||
+|| 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) ||

|| -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 ||
-Line 35:
+Line 38:
-|| out vol || output volume || ||
+|| out vol || output volume ||
-Line 44:
+Line 47:
-description
+{{{

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.