:orphan: .. _ahelp_3dinfill: ******** 3dinfill ******** .. contents:: :local: | .. code-block:: none 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