Differences between revisions 2 and 3

Name

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

Synopsis

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

Arguments

Positional Arguments

<input MR directory>	input directory
<output MR directory>	output directory

Required Flagged Arguments

none

Optional Flagged Arguments

General

-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>	Talairach coords of the seed for the corpus callosum
-P <x> <y> <z>	Talairach coords of the seed for the pons
-lh <x> <y> <z>	Talairach coords of the white matter seed for the left hemisphere
-rh <x> <y> <z>	Talairach coords of the white matter seed for the right hemisphere

Alternative seed point options in voxel coordinates

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

Outputs

filled

The filled volume for the cortical reconstruction- used for subsequent surface tesselation.

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

Links

FreeSurfer, FsFast

Methods Description

References

Reporting Bugs

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

Author/s

BruceFischl

-Deletions are marked like this.
+Additions are marked like this.
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-mri_fill - Creates hemispheric cutting planes and fills white matter with specific values for subsequent surface tesselation.
+mri_fill - creates hemispheric cutting planes and fills white matter with specific values for subsequent surface tesselation
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-usage: mri_fill [options] <input MR directory> <output MR directory>
+mri_fill [options] <input MR directory> <output MR directory>
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+|| <input MR directory> || input directory ||

|| <output MR directory> || output directory ||
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+none
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-        -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
+=== General ===

|| -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> || Talairach coords of the seed for the corpus callosum||

||-P <x> <y> <z> || Talairach coords of the seed for the pons||

||-lh <x> <y> <z>  || Talairach coords of the white matter seed for the left hemisphere||

||-rh <x> <y> <z>  || Talairach coords of the white matter seed for the right hemisphere||



=== Alternative seed point options in voxel coordinates ===

|| -CV <x> <y> <z> || voxel coords of the seed for the corpus callosum||

|| -PV <x> <y> <z> || voxel coords of the seed for the pons||
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+??
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-None
+??
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-["mri_segment"],
+["mri_segment"]
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+??
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+??