classify
classify voxels in MRI volumes into tissue classes
classify [options] <input_volumes> <output.mnc>
DESCRIPTION
classify classifies voxels in one or more MINC input volumes into tissue classes using a variety of supervised and unsupervised classification algorithms. Supported classifiers include minimum distance, K-nearest neighbours (KNN), artificial neural network (ANN), hard C-means (HCM), fuzzy C-means (FCM), and Bayesian classification. Training data can be provided via tag files. Fuzzy classification outputs can be written as separate volumes for each tissue class.
OPTIONS
-verbose- Print progress information.
-debug- Print debugging information.
-clobber- Overwrite an existing output file.
-byte- Store output with 8-bit integer voxels.
-short- Store output with 16-bit integer voxels.
-long- Store output with 32-bit integer voxels.
-float- Store output with 32-bit floating point voxels.
-double- Store output with 64-bit floating point voxels.
-signed- Store output with signed integer voxels.
-unsigned- Store output with unsigned integer voxels.
-output_range- Specify the output intensity range.
-tagfile- Specify a tag file containing training samples.
-volume- Specify the volume index for training.
-class_names- Specify class names for the classifier.
-load_train- Load a previously saved training set.
-save_train- Save the training set for later use.
-train_only- Only perform training; do not classify.
-parameter- Specify classifier parameters.
-apriori- Specify a priori probability volumes for each class.
-fuzzy- Enable fuzzy classification output.
-fprefix- Set the prefix for fuzzy output filenames.
-fpath- Set the path for fuzzy output files.
-fuzzy_voxel_min- Set the minimum fuzzy membership for a voxel.
-fuzzy_voxel_max- Set the maximum fuzzy membership for a voxel.
-fuzzy_image_min- Set the minimum fuzzy membership for an image.
-fuzzy_image_max- Set the maximum fuzzy membership for an image.
-fbyte- Store fuzzy output with 8-bit integer voxels.
-fshort- Store fuzzy output with 16-bit integer voxels.
-flong- Store fuzzy output with 32-bit integer voxels.
-ffloat- Store fuzzy output with 32-bit floating point voxels.
-fdouble- Store fuzzy output with 64-bit floating point voxels.
-mask- Specify a mask volume for restricting classification.
-user_mask_value- Set the mask value for voxel inclusion.
-user_mask_class- Set the mask class for voxel inclusion.
-nocache- Do not use volume caching.
-max_cache_size- Set the maximum cache size in bytes.
-block_sizes- Set the block sizes for caching.
-min- Use the minimum distance classifier.
-knn- Use the K-nearest neighbours classifier.
-ann- Use the artificial neural network classifier.
-hcm- Use the hard C-means classifier.
-fcm- Use the fuzzy C-means classifier.
-bayes- Use the Bayesian classifier.
EXAMPLES
classify -tagfile training.tag t1.mnc classified.mnc
classify -knn -tagfile training.tag -mask brain_mask.mnc t1.mnc t2.mnc pd.mnc classified.mnc
classify -fcm -fuzzy -fprefix fuzzy_ t1.mnc classified.mnc
AUTHOR
Jason Lerch - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © 2002 by Jason Lerch