Index TableOfContents

Name

mri_fill - Creates hemispheric cutting planes and fills white matter with specific values for subsequent surface tesselation.

Synopsis

usage: mri_fill [options] <input MR directory> <output MR directory>

Arguments

Positional Arguments

Required Flagged Arguments

Optional Flagged Arguments

• -T <threshold> - specify fill_holes threshold (default=1) -xform <xformname> - use xform dst offset to get an accurate Talairach volume

Seed point options in Talairach coordinates:

• -C <x> <y> <z> - the Talairach coords of the seed for the corpus callosum -P <x> <y> <z> - the Talairach coords of the seed for the pons -lh <x> <y> <z> - the Talairach coords of the white matter seed

  • for the left hemisphere

  -rh <x> <y> <z> - the Talairach coords of the white matter seed

  • for the right hemisphere

Alternative seed point options in voxel coordinates:

• -CV <x> <y> <z> - the voxel coords of the seed for the corpus callosum -PV <x> <y> <z> - the voxel coords of the seed for the pons

Outputs

Description

Examples

Example 1

mri_fill SUBJECT/mri/wm/. SUBJECT/mri/filled

Takes a subjects wm volume as input and uses this to find cutting planes to seperate the hemispheres and remove the brainstem, and fills hemispheres with specific values as filled volume output.

Bugs

None

See Also

["mri_segment"],

Links

FreeSurfer, FsFast

Methods Description

References

Reporting Bugs

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

Author/s

BruceFischl