AFNI program: 3dinfill
Output of -help
A program to fill holes in a volumes.
3dinfill <-input DSET>
-input DSET: Fill volume DSET
-prefix PREF: Use PREF for output prefix.
-Niter NITER: Do not allow the fill function to do more than NITER
passes. A -1 (default) lets the function go to a maximum
of 500 iterations. You will be warned if you run our of
iterations and holes persist.
-blend METH: Sets method for assigning a value to a hole.
MODE: Fill with most frequent neighbor value. Use MODE when
filling integral valued data such as ROIs or atlases.
AVG: Fill with average of neighboring values.
AUTO: Use MODE if DSET is integral, AVG otherwise.
SOLID: No blending, brutish fill. See also -minhits
SOLID_CLEAN: SOLID, followed by removal of dangling chunks
Dangling chunks are defined as non-zero regions
that surround lesser holes, i.e. holes that have
less than MH. The cleanup step is not iterative
though, and you are most likely better off using
option -ed to do the cleanup.
-minhits MH: Crietrion for considering a zero voxel to be a hole
MH refers to the total number of directions alogn which a
zero voxel is considered surrounded by non zero values.
a value of 1 is the least strict criterion, and a value of 3
is the strictest.
This parameter can only be used with -blend SOLID
-ed N V: Erode N times then dialate N times to get rid of hanging chunks.
Values filled in by this process get value V.
-mask MSET: Provide mask dataset to select subset of input.
-mask_range BOT TOP: Specify the range of values to consider from MSET.
Default is anything non-zero.
-mrange BOT TOP: Same as option -mask_range
-cmask CMASK: Provide cmask expression. Voxels where expression is 0
are excluded from computations. For example:
-cmask '-a T1.div.r+orig -b T1.uni.r+orig -expr step(a/b-10)'
NOTE: For the moment, masking is only implemented for the SOLID* fill
Starting from a whole head mask that has some big holes in it where CSF and
cavities are. Fill the inside of the mask and remove dangling chunks in the
end with -ed
3dinfill -blend SOLID -ed 3 1 -prefix filledmask \
-minhits 2 -input holymask+orig.
This program will be slow for high res datasets with large holes.
If you are trying to fill holes in masks, consider also:
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Sun Mar 7 20:05:47 EST 2021