A program to fill holes in a volumes.
3dinfill <-input DSET>
Options:
-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
- method.
Example 1: 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:
3dmask_tool -fill_holes