Image segmentation (MABS) command file reference

The mabs parameter file can have seven sections: PREALIGNMENT, ATLAS-SELECTION, TRAINING, REGISTRATION, STRUCTURES, LABELING and OPTIMIZATION_RESULT. Each section contatins specific entries that can not be mixed. All the possible parameters are listed below:

Option	Section	Default value	Possible values	Description
mode	PREALIGNMENT	disabled	disabled, default, custom	Set the method for prealign the images
reference	PREALIGNMENT	not set		Set the reference image
spacing	PREALIGNMENT	not set		Set the reference spacing
registration_config	PREALIGNMENT	not set	plastimatch registration file without the GLOABL section	Set the registration parmameters for prealign if “custom” mode is chosen
prealign_struct	PREALIGNMENT	not set	name of an atlas structure	Use the specified structure to execute center of gravity initialization
enable_atlas_selection	ATLAS-SELECTION	false	true, false	Enable atlas selection process
atlas_selection_criteria	ATLAS-SELECTION	nmi	nmi, nmi-post, nmi-ratio, mse, mse-post, mse-ratio, random, precomputed	Set the criterion to use for ranking the atlases (see at the bottom of this page for further explanations)
similarity_percent_threshold	ATLAS-SELECTION	0.40	Ranging from 0.0 to 1.0	Percentage threshold used to pick the atlases from the ranking obtained on the basis of a nmi/mse similarity value. All the atlases having a similarity value greater equal to the following value will be selected. minimum_similarity_percentage_value = similarity_min + (threshold * (similarity_max - similarity_min))
atlases_from_ranking	ATLAS-SELECTION	-1 (means disabled)	ranging from 0 to the whole number of atlases	Number of atlases to pick from the ranking (nmi/mse based or precomputed).
mi_histogram_bins	ATLAS-SELECTION	100	as usual for mi histogram bins setting	Set the number of histogram bins to use for nmi computation
percentage_nmi_random_sample	ATLAS-SELECTION	not set by plastimatch, itk default value is used	between 0 (not included) and 1 (included)	Set the number of random voxels to use for NMI computation. The final value is equal to the number of voxels of fixe images time the set value.
roi_mask	ATLAS-SELECTION	not set	image file name (.mha/.mhd/.nii.gz/.nrrd/ecc)	Set the mask to reduce the volume of the subject/atlas images where the nmi/mse will be computed
selection_reg_parms	ATLAS-SELECTION	not set	plastimatch registration file without the GLOABL section	File where are stored the registration parameters (without GLOBAL stage) that will be used for the nmi-post, nmi-ratio mse-post and mse-ratio selection
lower_mi_value_subject	ATLAS-SELECTION	not set	in the range of the intesities of the subject image. Anyway lower than the upper_mi_value_subject	Lower intensity bound on the histogram of the subject image. Only the values greater than this threshold will be used for nmi computation
upper_mi_value_subject	ATLAS-SELECTION	not set	in the range of the intesities of the subject image. Anyway higher than the lower_mi_value_subject	Upper intensity bound on the histogram of the subject image. Only the values lower than this threshold will be used for nmi computation
lower_mi_value_atlas	ATLAS-SELECTION	not set	in the range of the intesities of the atlas image. Anyway lower than the upper_mi_value_atlas	Lower intensity bound on the histogram of the atlas image. Only the values greater than this threshold will be used for nmi computation
upper_mi_value_atlas	ATLAS-SELECTION	not set	in the range of the intesities of the atlas image. Anyway higher than the lower_mi_value_atlas	Upper intensity bound on the histogram of the atlas image. Only the values lower than this threshold will be used for nmi computation
min_random_atlases	ATLAS-SELECTION	6	ranging from 1 to the whole number of atlases. Anyway equal/lower than max_random_atlases	Minimum number on atlases to extract when random selection is choosen
max_random_atlases	ATLAS-SELECTION	14	ranging from 1 to the whole number of atlases. Anyway equal/greater than min_random_atlases	Maximim number on atlases to extract when random selection is choosen
precomputed_ranking	ATLAS-SELECTION	note set	text file where a precomputed ranking was stored	Text file containing the precomputed ranking. For each line there is a ranking for an patient. The style is: patient1: atl1 atl2 atl3 atl4
training_dir	TRAINING	not set	folder path	Folder that contains the data for the training
fusion_criteria	TRAINING	gaussian	“gaussian”, “staple”, “gaussian,staple” and “none”	Labels fusion criterion
distance_map_algorithm	TRAINING	not set		Implementation for distance map computation
minsim_values	TRAINING	L 0.0001:1:0.0001		Minimum similarity values for gaussian labels fusion
rho_values	TRAINING	1:1:1		Rho values for gaussian labels fusion
sigma_values	TRAINING	L 1.7:1:1.7		Sigma values for gaussian labels fusion
threshold_values	TRAINING	0.5		Threshold values for gaussian labels fusion
write_distance_map_files	TRAINING	1 (true)	0 (false) or 1 (true)	Write distance map files on the disk (only for gaussian fusion)
write_thresholded_files	TRAINING	1 (true)	0 (false) or 1 (true)	Write thresholded files on the disk (only for gaussian fusion)
write_weight_files	TRAINING	1 (true)	0 (false) or 1 (true)	Write weight files on the disk (only for gaussian fusion)
write_warped_images	TRAINING	1 (true)	0 (false) or 1 (true)	Write warped images on the disk
write_warped_structures	TRAINING	1 (true)	0 (false) or 1 (true)	Write warped structures on the disk
confidence_weight	TRAINING	1.0		Multiplicative factor for the prior probability that any pixel would be classified as inside the structure (only for staple fusion)
registration_config	REGISTRATION	not set	plastimatch registration file without the GLOABL section	Set the registration parmameters for the deformable registration
no predefined entries, just the list of the structures to segment (without extension file)	STRUCTURES	not set
input	LABELING	not set
output	LABELING	not set
registration	OPTIMIZATION_RESULT	not set
gaussian_weighting_voting_rho	OPTIMIZATION_RESULT	1.0
gaussian_weighting_voting_sigma	OPTIMIZATION_RESULT	30.0
gaussian_weighting_voting_minsim	OPTIMIZATION_RESULT	0.3
optimization_result_confidence_weight	OPTIMIZATION_RESULT	1.0
gaussian_weighting_voting_thresh	OPTIMIZATION_RESULT	0.4

The possible atlas selection criteria are nmi, nmi-post, nmi-ratio, mse, mse-post, mse-ratio, random, precomputed.

Criterion	Description
nmi	Normalized mutual information computed between prealigned (ridgly) images
nmi-post	Normalized mutual information computed between images after a deformable registration
nmi-ratio	Score calculated using the normalized mutual information computed before and after a deformable registration
mse	Root mean square error computed between prealigned (ridgly) images
mse-post	Root mean square error computed between images after a deformable registration
mse-ratio	Score calculated using the root mean square error computed before and after a deformable registration
random	Random selection of a random number of atlases
precomputed	Ranking read from a text file containing a precomputed list of atlases

Structure name mapping

It is required to put the name of each structure to be segmented into the STRUCTURES section. If structure names are uniformly defined, then you simply need to list them:

[STRUCTURES]
Prostate
Bladder
Rectum

If the structure names are not uniform, you can use this section to map multiple names (within an atlas) to the same target name. To do so, put the target name to the left of the equal sign, and the original name to the right of the equal sign. For example, the following would map three different spellings to the same target name:

[STRUCTURES]
Prostate
Prostate=prostate
Prostate=Pros_GTV