minc-toolkit documentation project

This is collection of documentation files for various minc tools. It was auto-converted from the legacy .man files to github-style markup format and then manually corrected.

MINC Core Tools

• mincinfo - print out general information about a minc file
• mincheader - print out complete header information for a minc file
• mincstats - calculate simple statistics across voxels of a minc file
• mincdiff - report differences between minc files
• voxeltoworld - convert voxel coordinates to world coordinates
• worldtovoxel - convert world coordinates to voxel coordinates
• minchistory - display the history of processing steps applied to a MINC file
• mincpik - generate image files from MINC volumes
• minccomplete - check if a MINC or xfm file has been completely written
• mincmorph - perform morphological operations on MINC volumes

File Format Conversion

• rawtominc - converts a stream of binary image data to a minc format file
• mincconvert - convert between MINC 1 to MINC 2 format
• dcm2mnc - convert sets of DICOM files to one or more MINC format files
• ecattominc - convert an ecat format file (version 6.x or 7.x) to a minc format file
• minctoecat - convert a minc format file to an Ecat7 format file
• minctoraw - copy data from a MINC file
• mnc2nii - convert a MINC format file to a NIfTI-1 or Analyze format file
• nii2mnc - convert a NIfTI-1 or Analyze 7.5 format file to a MINC format file
• upet2mnc - convert a Concorde microPET format file to a MINC format file
• vff2mnc - convert set of vff file(s) to one 3D MINC2.0 format file
• mri_to_minc - convert various MRI scanner formats to MINC format
• ecat2hdf5 - convert ECAT format PET data to HDF5 format

Low-Level File Manipulation

• minc_modify_header - modify the attributes in the header of a minc file
• minccopy - copy minc image values from one minc file to another
• mincdump - convert minc files to ASCII form (CDL)
• mincedit - edit a MINC file header
• mincexpand - expands a compressed minc file, if necessary
• mincextract - dump a hyperslab of MINC file data
• invert_raw_image - invert 2D image along either or both axes
• mincgen - generate a MINC file from a CDL file
• mincdefrag - remove small disconnected fragments from a labelled MINC volume

Mathematical Operations on Voxel Level

• minccalc - perform complex math operations on minc files
• minccmp - compare one or more minc file using comparator operators
• minclookup - perform lookup table conversions on minc files
• mincmakescalar - convert vector minc files to scalar
• mincmakevector - convert a list of scalar minc files into one vector file
• mincmath - perform simple math operations on minc files
• mincwindow - limit voxel values to a given range

Volume Operations

• mincaverage - average minc files
• mincblur - convolve an input volume with a Gaussian blurring kernel
• mincresample - resamples a minc file along new spatial dimensions
• mincreshape - cuts a hyperslab out of a minc file (with dimension re-ordering)
• mincsample - generate samplings from minc files
• autocrop - tool for extracting and manipulating bounds of a MINC file
• mincblob - calculate blobs from minc deformation grids
• mincconcat - concatenate minc files along a specific dimension
• mincbbox - calculate the bounding box of non-zero data in a MINC volume
• mincmask - apply a binary mask to a MINC volume
• mincskel - compute the skeleton (medial surface) of a white matter partial volume estimate
• minctotag - convert labelled voxels in a MINC volume to a tag point file
• autocrop_volume - crop a MINC volume by removing outer voxels below a threshold
• average_voxels - average voxels in blocks within a MINC volume
• box_filter_volume - apply a box filter (uniform averaging) to a MINC volume
• box_filter_volume_nd - apply an n-dimensional box filter to a MINC volume
• chamfer_volume - compute the chamfer distance transform of a binary volume
• clamp_volume - clamp voxel values in a MINC volume to a specified range
• cluster_volume - label connected components in a thresholded MINC volume
• copy_stats_to_volume - copy per-vertex statistics to a volume using a surface mapping
• count_thresholded_volume - count non-zero mask voxels corresponding to volume values within a threshold
• create_four_volumes - create four class volumes from multiple input volumes or tag files
• dilate_volume - dilate regions of a specified value in a MINC volume
• dilate_volume_completely - fully dilate regions of a specified value until no further dilation is possible
• evaluate - evaluate a volume at the vertices of a surface object
• find_image_bounding_box - find the bounding box of an RGB image excluding the background colour
• find_volume_centroid - find and print the centroid of a MINC volume
• flip_volume - interchange voxel values with their left-right opposites in a MINC volume
• histogram_volume - compute and output a histogram of voxel intensities in a MINC volume
• make_diff_volume - create a 4-class volume based on value ranges in two input volumes
• make_geodesic_volume - create a geodesic distance volume from a seed point in a MINC volume
• make_gradient_volume - compute gradient magnitude or second derivative of a MINC volume
• mask_volume - mask a MINC volume by setting voxels outside a specified mask range
• normalize_pet - intensity normalize a PET MINC volume
• preprocess_segmentation - preprocess a classified volume for cortical segmentation
• random_volume - generate a random volume matching a sample volume geometry
• random_warp - create a random warp (deformation) transform from a surface object
• scale_minc_image - scale voxel intensities in a MINC volume by a constant factor
• scan_object_to_volume - scan a BIC object into a MINC volume creating a binary mask
• subsample_volume - subsample a MINC volume by taking every nth voxel in each dimension
• threshold_volume - create a label volume by thresholding an input MINC volume
• transform_volume - apply a spatial transform to a MINC volume by modifying its voxel-to-world transform
• volume_object_evaluate - evaluate volume values at surface object vertex positions
• voldiff - compare classified volumes and produce a difference volume
• volume_cog - compute the intensity-weighted center of gravity of a MINC volume

Registration and Transformation

• minctracc - estimates the spatial transformation required to register two volumes together
• mritoself - intra-subject registration of two volumetric data sets
• mritotal - performs multi-scale fitting of a normal human brain to a standard model
• xfm2def - convert a MNI transform file to a deformation volume
• xfmconcat - concatenate MNI transform files
• xfminvert - invert an MNI transform file
• xfmflip - flip an MNI transform file
• transformtags - apply MNI transform to a tag file
• param2xfm - create a MNI transform file from rotation, translation, scale, and shear parameters
• xfm2param - extract rotation, translation, scale, and shear parameters from a MNI transform file
• xfmtool - manipulate MNI transformation files
• xfmdecomp - decompose a .xfm transformation into rotation, translation, scale, and shear
• cmpxfm - compare two MNI linear transform files element-by-element
• check_scale - check and correct the Z-scale of a MNI linear transform
• volume_cog - compute the intensity-weighted center of gravity of a MINC volume
• xcorr_vol - compute the normalized cross-correlation between two MINC volumes

Tag Point Tools

• transform_tags - apply a spatial transformation to a tag point file
• minctotag - convert labelled voxels in a MINC volume to a tag point file
• chop_tags - clip tag points to those within specified coordinate ranges
• clip_tags - clip tag points based on distance from a reference plane
• extract_tag_slice - extract tag points lying on a specified slice of a volume
• find_tag_outliers - identify tag points that deviate significantly from expected positions
• flip_tags - flip tags about the left-right centre of a volume
• interpolate_tags - interpolate tag points between two sets by a given ratio
• match_tags - find corresponding tag points between two tag files
• stats_tag_file - compute and display statistics for a tag file
• tag_volume - create a volume from tag points sampling at specified y-axis intervals
• tags_to_spheres - create sphere objects at tag point positions
• tagtominc - convert a tag file to a labelled MINC volume
• dump_points_to_tag_file - write surface object points to a tag file

Surface and Geometry Tools

• apply_sphere_transform - apply a spherical transform to a surface object
• blur_surface - blur a surface object using a Gaussian kernel
• coalesce_lines - coalesce shared points in a lines object
• compare_lengths - compare edge lengths between two polygon meshes
• contour_slice - create contour lines for a given slice of a volume
• convex_hull - create a convex hull polyhedron from a surface or volume
• create_2d_sheet - create a 2D sheet representation of a surface object
• create_2d_surface - create a 2D surface representation of a 3D surface object
• create_box - create a rectangular box object file
• create_landmark_full_volume - create a label volume from landmark tag files
• create_surface_interpolation_lsq - create a least-squares surface interpolation from scattered data
• create_warping_points - create warping tag points from surface correspondences
• extract_largest_line - extract the largest connected line from a line object
• find_buried_surface - find buried regions on a polygon surface based on curvature radius
• find_surface_distances - compute distances from a surface to threshold boundaries in a volume
• find_vertex - find a specific vertex in a surface object
• fit_3d - fit a deformable model to a MINC volume using surface deformation
• fit_curve - fit a smooth cubic spline curve to a set of points
• fit_curve2 - fit a piecewise linear curve to a set of points
• flatten_polygons - flatten a polygonal surface into 2D
• flatten_sheet - flatten a surface sheet to a 2D plane
• flatten_sheet3 - flatten a surface sheet to a 2D plane using topological or physical method
• flatten_to_sphere - map a surface onto a sphere
• flatten_to_sphere2 - map a surface onto a sphere with curvature and stretch weights
• make_grid_lines - create grid lines on a surface object
• make_line_links - create line segments linking two input line objects
• make_sphere_transform - create a spherical transform mapping for a surface
• make_surface_bitlist - create a surface bitlist volume from a thresholded MINC volume
• map_colours_to_sphere - map colours from a volume onto a spherical surface object
• map_sheets - map surface sheets between spherical and flat representations
• map_surface_to_sheet - map a 3D surface to a flat 2D sheet image
• marching_cubes - create a polygonal surface from a thresholded MINC volume using marching cubes
• plane_polygon_intersect - compute the intersection of a plane with a polygonal surface
• reparameterize_line - reparameterize a line object by redistributing points evenly
• spherical_resample - resample a surface using spherical parameterization
• trimesh_resample - subdivide and coalesce a triangular mesh
• trimesh_set_points - set vertex positions in a triangular mesh from another mesh or object
• trimesh_to_polygons - convert a triangular mesh to a triangular mesh to a polygons file
• two_surface_resample - resample a surface using two model surfaces

Label and Classification Tools

• add_labels - add or modify value-label pairs in a MINC volume
• classify_sulcus - classify sulcal regions on a cortical surface
• clean_surface_labels - correct labels on a surface object
• create_label_map - create a label map volume from a template
• diff_mahalanobis - compute the difference in Mahalanobis distances between two groups
• label_sulci - label sulcal regions on a cortical surface using reference sulcal points and value ranges
• labels_to_rgb - convert label values to RGB colour values using a lookup table
• lookup_labels - list or look up value-label pairs in a MINC volume
• print_all_label_bounding_boxes - print voxel counts and bounding boxes for each label in a MINC volume
• print_all_labels - print voxel counts for each label in a MINC volume

Statistical and Analysis Tools

• compare_left_right - compare left and right hemispheres of surface objects
• compare_left_right_groups - compare left-right hemisphere differences between groups of surface objects
• compute_resels - compute resolution elements (resels) from cortical surface meshes
• dump_deformation_distances - dump deformation distances from a non-linear transformation
• dump_rms - compute and dump RMS distance between two surfaces
• dump_transform - dump the voxel-to-world transform of a MINC volume to an .xfm file
• dump_uv - dump UV texture coordinates of a surface object
• f_prob - compute F-statistic probability values
• find_peaks - find local maxima (peaks) in a MINC volume
• gaussian_blur_peaks - create a volume from Gaussian-blurred peak locations
• get_tic - compute statistics for spherical regions in a MINC volume
• group_diff - compute group differences and F-statistics from surface data files
• intensity_statistics - compute intensity statistics within labelled regions of a volume
• mask_values - mask values in a volume based on a range in another volume
• print_2d_coords - print 2D coordinates corresponding to a 3D point on a surface
• print_axis_angles - print angles between native and Talairach axes
• print_volume_value - print the voxel value at a given world coordinate in a volume
• print_world_value - print the voxel value at a given world coordinate in a volume
• print_world_values - evaluate volume values at multiple world coordinates from a file
• regional_thickness - compute regional cortical thickness statistics from per-vertex data

Image Composition and Visualization

• composite_images - composite multiple RGB images into a single output
• composite_minc_images - composite two MINC images
• composite_volumes - composite multiple MINC volumes into a single volume
• compute_bounding_view - compute the world limits of an object in an orthogonal view
• concat_images - concatenate two RGB images into one
• dim_image - darken an RGB image by a given strength factor
• make_slice - extract a 2D slice from a MINC volume as an image
• minc_to_rgb - convert a MINC volume to an RGB image
• place_images - place multiple RGB images at specified positions in an output image
• rgb_to_minc - convert RGB images to a MINC volume

Non-Uniformity Correction

• correct_field - apply a bias field correction to a MINC volume using a mask
• evaluate_field - evaluate a compact spline field representation and write it as a MINC volume
• extracttag - extract tag points from a probability mask volume
• field2imp - convert a bias field MINC volume to an IMP format compact representation
• imp2field - convert an IMP format compact representation to a bias field MINC volume
• make_template - create a sampling template volume for N3 non-uniformity correction
• nu_correct - correct intensity non-uniformity artifacts in MRI volumes
• nu_estimate - estimate the non-uniformity field in an MRI volume
• nu_estimate_np_and_em - estimate non-uniformity using non-parametric and EM methods
• nu_evaluate - evaluate and apply a non-uniformity correction to an MRI volume
• resample_labels - resample a labelled MINC volume to match a template
• sharpen_hist - create a mapping for minclookup to sharpen a volume histogram
• sharpen_volume - apply histogram sharpening to a MINC volume
• spline_smooth - smooth and extrapolate data in MINC volumes using spline fitting
• volume_hist - create histograms of intensity values in a MINC volume
• volume_stats - compute and print statistics for a MINC volume

Intensity Normalization

• headmask - create a head mask for MRI intensity normalization
• inormalize - intensity normalize a MINC volume following a registered model volume
• lgmask - create a large-structure brain mask for intensity normalization
• normalize_mri - normalize MRI intensity values using a standard approach
• nu_correct_norm - perform combined non-uniformity correction and intensity normalization

Classification

• classify - classify voxels in MRI volumes into tissue classes
• crispify - create a crisp labelled volume from multiple fuzzy classification volumes
• voldiff - compare classified volumes and produce a difference volume

MRF Segmentation

• gamixture - genetic algorithm for Gaussian mixture model parameter optimization
• mrfseg - MRF-based brain tissue segmentation
• mrfseg.pl - MRF-based tissue segmentation pipeline

EZminc Analysis Tools

• dircos_to_xfm - convert direction cosines to an .xfm transformation file
• em_classify - classify voxels using expectation-maximization algorithm
• fast_blur - fast Gaussian blurring of a MINC volume
• fdr_threshold - compute False Discovery Rate (FDR) threshold for statistical maps
• minc_anlm - adaptive non-local means denoising of MRI images
• minc_downsample - downsample a MINC volume by specified factors
• minc_nuyl - intensity normalization using piece-wise linear histogram matching
• minc_rank - convert voxel intensities to rank values in the range 0-100
• minc_taylor_reg - apply Taylor series-based registration using vector coefficient volumes
• noise_estimate - estimate noise level in MRI volumes
• sharpness_estimate - estimate image sharpness based on median gradient magnitude
• t2_fit - fit T2 relaxation curves from multiple echo images
• volume_dwt - perform forward or backward discrete wavelet transform on a MINC volume
• volume_pol - polynomial intensity normalization between volumes

EZminc Volume Similarity

• fuzzy_volume_similarity - calculate fuzzy volume similarity metrics for tissue probability maps
• multiple_volume_similarity - calculate multiple volume discrete label similarity (GTC) metrics
• volume_gtc_similarity - calculate generalized Tanimoto coefficient and overlap metrics for discrete labels
• volume_similarity - calculate volume similarity metrics for binary label volumes

EZminc PCA and Linear Modelling

• grids_pca - perform principal component analysis on deformation grid files
• volumes_lm - compute per-voxel linear models from a training list of volumes
• volumes_lsq - compute per-voxel least-squares decomposition using linear model components
• volumes_pca - perform principal component analysis on a set of MINC volumes
• volumes_pca_preprocess - preprocess volumes for PCA analysis

EZminc Registration Scripts

• bestlinreg.pl - perform best linear registration between two MINC volumes
• bestlinreg_g - perform best linear registration (generalized variant)
• bestlinreg_s - perform best linear registration (symmetric variant)
• bestlinreg_s2 - perform best linear registration (symmetric variant 2)
• nlfit_f - non-linear fitting at fine resolution step
• nlfit_l - non-linear fitting at large/coarse resolution step
• nlfit_o2 - non-linear fitting optimization pass 2
• nlfit_s - non-linear fitting at standard resolution step

EZminc QC and Visualization Scripts

• minc_aqc.pl - automated quality control assessment of MINC volumes
• minc_pretty_pic.pl - generate publication-quality images from MINC volumes
• minc_pretty_pic_m.pl - generate publication-quality montage images from MINC volumes
• minc_qc.pl - generate quality control images from MINC volumes
• minc_qc2.pl - generate quality control images from MINC volumes (version 2)
• minc_qc_rgb.pl - generate RGB quality control images from MINC volumes
• minc_qc_t2t1.pl - generate T2/T1 overlay quality control images

EZminc Utility Scripts

• deface_minipipe.pl - defacing mini-pipeline for anonymizing MRI volumes
• deface_volume.pl - deface (remove facial features from) a MINC volume
• icc_mask.pl - create an intra-cranial cavity mask for brain volume estimation
• lobe_segment.pl - segment brain lobes using atlas-based label propagation
• lobes_to_volumes.pl - compute lobe volumes from a lobe-segmented MINC volume
• make_face.pl - extract a face surface from an MRI volume
• make_random_grid.pl - generate a random deformation grid for testing
• uniformize_minc.pl - resample a MINC volume to a uniform axis-aligned grid
• volume_denoise.pl - NLM-based volume denoising with automatic noise estimation
• xfm_normalize.pl - normalize an XFM or grid transform to a standard uniform axis-aligned format

EZminc Analysis Tools (Additional)

• resample_grid - apply an arbitrary transform to a deformation grid
• tag2csv - convert a MINC .tag file into comma-separated values (CSV)

ITK Image Processing

• itk_convert - convert between medical image formats using ITK (MINC, NIfTI, NRRD, etc.)
• itk_convert_xfm - convert transformation files between ITK and MINC .xfm formats
• itk_diffusion - apply anisotropic diffusion filtering to a volume
• itk_distance - calculate a distance transform on a volume
• itk_fill_hole - apply hole-filling operation to a volume
• itk_g_morph - perform gray-scale morphological operations on a volume
• itk_laplace - apply Laplacian of Gaussian filter to a volume
• itk_laplacian_sharpening - apply Laplacian sharpening filter to a volume
• itk_morph - perform binary morphological image operations (dilate, erode, open, close)
• itk_resample - resample a MINC volume using ITK with spline interpolation and .xfm transforms
• itk_similarity - calculate various ITK image similarity metrics between two volumes
• itk_vesselness - apply vesselness filter for vessel-like structure enhancement

Deformable Registration

• DemonsRegistration - diffeomorphic demons registration between two volumes
• LogDomainDemonsRegistration - log-domain diffeomorphic demons registration between two volumes
• grid_2_log - convert deformation field to log-domain velocity field (or compute exponent)
• grid_proc - perform operations on deformation grids: log, exp, magnitude, determinant, inverse
• grid_statistics - compute statistics on deformation grid: Jacobian, harmonic energy, magnitude
• log_resample - resample image using log-domain vector field transforms

Distortion Correction

• adni_preprocess.pl - preprocess ADNI images for distortion correction analysis
• c_fit_harmonics_grids - fit cylindrical harmonic coefficients to deformation grids for distortion correction
• c_param2grid - convert cylindrical harmonic parameters to deformation grid
• calc_distortions.pl - calculate geometric distortion fields from phantom measurements
• fit_harmonics_grids - fit spherical harmonic coefficients to deformation grids
• fit_harmonics_grids_diff - spherical harmonic fitting using paired linear/nonlinear transform differentials
• fit_harmonics_grids_regularize - spherical harmonic fitting with Legendre polynomial regularization
• lego_core_extract.pl - extract core markers from a LEGO phantom scan
• par2xfm.pl - convert distortion parameters to an XFM grid transform
• param2grid - convert spherical harmonic parameters to deformation grid
• phantom_distortion_measure.pl - calculate geometric distortion from phantom scans via hierarchical nonlinear registration
• phantom_distortion_measure_v2.pl - measure geometric distortion using paired phantom scan and mask inputs (version 2)
• phantomfit.pl - hierarchical nonlinear fitting constrained by spherical harmonics using minctracc
• phantomfit_ANTS.pl - hierarchical nonlinear fitting constrained by spherical harmonics using ANTs
• phantomfit_DD.pl - hierarchical nonlinear fitting constrained by spherical harmonics using Diffeomorphic Demons
• phantomfit_elastix.pl - hierarchical nonlinear fitting constrained by spherical harmonics using Elastix

Patch-Based Morphology

• hcag_segmentation_pipeline.pl - run hippocampus and amygdala segmentation pipeline
• itk_merge_discrete_labels - merge multiple discrete label volumes by overlay (non-zero overwrite)
• itk_merge_labels - merge multiple probability maps into a single label image by maximum probability voting
• itk_minc_nonlocal_filter - patch-based non-local means denoising
• itk_patch_grading - patch-based non-local grading using SVM, NNLS, or exponential weighting
• itk_patch_morphology - patch-based segmentation using expert priors (Coupe et al. 2010)
• itk_patch_morphology_mc - multi-channel patch-based segmentation
• itk_patch_segmentation - perform patch-based label fusion segmentation
• itk_split_labels - split discrete label volume into per-label probability volumes with anti-aliasing
• patch_segmentation_pipeline.pl - RASCAL patch-based label fusion segmentation pipeline
• snipe_grading_pipeline.pl - SNIPE grading pipeline for Alzheimer’s disease classification
• ventricles_segmentation_pipeline.pl - ventricle segmentation pipeline using patch-based methods
• volume_patches - legacy non-local patch-based segmentation using MINC1 I/O

BIC Processing Pipelines

• pipeline_classify.pl - brain tissue classification using classify_clean
• pipeline_dbm.pl - deformation-based morphometry from nonlinear transforms
• pipeline_deface.pl - defacing pipeline for anonymizing MRI data
• pipeline_deface_grid.pl - generate a random distortion grid for defacing
• pipeline_em_classify.pl - EM-based brain tissue classification
• pipeline_face.pl - FACE anatomical feature extraction pipeline
• pipeline_jacobian.pl - compute Jacobian determinant from a nonlinear deformation grid
• pipeline_launch_all_segment.pl - launch all segmentation pipeline variants for a subject visit
• pipeline_launch_pve.pl - launch all partial volume estimation pipeline variants
• pipeline_longitudinal.pl - longitudinal brain analysis pipeline
• pipeline_mritotal.pl - stereotaxic registration pipeline with BEaST brain masking
• pipeline_nlr.pl - nonlinear registration pipeline
• pipeline_pve.pl - partial volume estimation pipeline
• pipeline_qc.pl - generate QC images for T1/mask and T1/T2 overlays
• pipeline_qc_face.pl - generate QC face renderings from three angles
• pipeline_qc_nl.pl - generate QC images for nonlinear classification and lobe segmentation
• pipeline_qc_reg.pl - generate QC image for nonlinear registration quality
• pipeline_qc_t1w.pl - generate QC image for T1w in Talairach space with outline overlay
• pipeline_qc_t2t1.pl - generate QC image for T1/T2 co-registration overlay
• pipeline_relx.pl - T2 relaxometry fitting from multiple echo volumes
• pipeline_relx_cls.pl - T2 relaxometry-based tissue classification
• pipeline_segment.pl - lobe segmentation using atlas templates
• pipeline_smooth.pl - smooth tissue probability maps with optional Jacobian modulation
• pipeline_t2tot1.pl - register T2/PD to T1 in Talairach space
• pipeline_tal_mask.pl - apply brain mask to T1/T2/PD volumes in Talairach space
• pipeline_talnoscale.pl - remove scaling from Talairach transform and resample
• pipeline_thomas.pl - tissue-class Jacobian-modulated blurred maps for THOMAS
• pipeline_volumes_lin.pl - compute brain tissue volumes from linear registration
• pipeline_volumes_nl.pl - compute brain and lobe volumes from nonlinear registration
• pipeline_watermark.pl - apply a visible watermark to an MRI volume

Registration Scripts

• compute_icbm_vols - compute ICBM volumes from a classified image
• mritotal_suppress - suppress fat signal from MRI data during mritotal registration
• multispectral_stx_registration - perform stereotaxic registration using multi-spectral MRI data
• nlfit_smr - perform non-linear fitting with surface-based multi-resolution
• remap_to_lobes - remap a detailed segmentation label file to lobe-level labels
• smooth_mask - smooth a binary mask volume
• sphere_resample_obj - resample a surface object onto a standard sphere tessellation
• suppress_fat - suppress fat signal in MRI volumes

Brain Extraction

• mincbeast - BEaST brain extraction tool
• beast_normalize - preprocess and normalize a MINC volume for BEaST brain extraction
• beast_prepareADNIlib - prepare an ADNI library for use with BEaST brain extraction

Visual Tools

• Display - interactive 3D visualization of MINC volumes and surface objects
• mincview - view a MINC file (primitive viewer)
• register - interactive volume display and point tagging program
• ray_trace - render 3D surface objects using ray tracing
• xdisp - an image display utility for the X Window System
• postf - a medical image display utility

Noise Filtering

• minc_anlm - adaptive non-local means denoising of MRI images
• mincnlm - non-local means denoising filter for MINC volumes

Registration Scripts

• mritoself - intra-subject registration of two volumetric data sets
• mritotal - performs multi-scale fitting of a normal human brain to a standard model
• minctracc - estimates the spatial transformation required to register two volumes together
• check_scale - check and correct the Z-scale of a MNI linear transform
• param2xfm - create a MNI transform file from rotation, translation, scale, and shear parameters
• xfm2param - extract rotation, translation, scale, and shear parameters from a MNI transform file
• xfmtool - manipulate MNI transformation files
• xfmdecomp - decompose a .xfm transformation into rotation, translation, scale, and shear
• xfmconcat - concatenate MNI transform files
• xfminvert - invert an MNI transform file
• xfmflip - flip an MNI transform file
• cmpxfm - compare two MNI linear transform files element-by-element
• xcorr_vol - compute the normalized cross-correlation between two MINC volumes
• volume_cog - compute the intensity-weighted center of gravity of a MINC volume
• mincbbox - calculate the bounding box of non-zero data in a MINC volume

Miscellaneous Tools

• ecat2hdf5 - convert ECAT format PET data to HDF5 format
• xfmdecomp - decompose a .xfm transformation into rotation, translation, scale, and shear
• make_model - create a model for use with mritotal
• make_phantom - create a synthetic MINC volume containing a geometric phantom object

Registration

• check_scale - check and correct the Z-scale of a MNI linear transform
• cmpxfm - compare two MNI linear transform files element-by-element
• mincchamfer - compute the chamfer distance transform of a MINC volume
• minctracc - estimates the spatial transformation required to register two volumes together
• param2xfm - create a MNI transform file from rotation, translation, scale, and shear parameters
• volume_cog - compute the intensity-weighted center of gravity of a MINC volume
• xfm2param - extract rotation, translation, scale, and shear parameters from a MNI transform file
• xfmtool - manipulate MNI transformation files
• xcorr_vol - compute the normalized cross-correlation between two MINC volumes

Statistical Analysis

• glim_image - fit a generalized linear model to voxel intensities across MINC volumes

Uncategorized

• autocrop - tool for extracting and manipulating bounds of a MINC file
• dcm2mnc - convert sets of DICOM files to one or more MINC format files
• ecattominc - convert an ecat format file (version 6.x or 7.x) to a minc format file
• invert_raw_image - invert 2D image along either or both axes
• minc_modify_header - modify the attributes in the header of a minc file
• mincaverage - average minc files
• mincbbox - calculate the bounding box of non-zero data in a MINC volume
• mincbeast - BEaST brain extraction tool
• mincblob - calculate blobs from minc deformation grids
• mincblur - convolve an input volume with a Gaussian blurring kernel
• minccalc - perform complex math operations on minc files
• minccmp - compare one or more minc file using comparator operators
• mincconcat - concatenate minc files along a specific dimension
• mincconvert - convert between MINC 1 to MINC 2 format
• minccopy - copy minc image values from one minc file to another
• mincdiff - report differences between minc files
• mincdump - convert minc files to ASCII form (CDL)
• mincedit - edit a MINC file header
• mincexpand - expands a compressed minc file, if necessary
• mincextract - dump a hyperslab of MINC file data
• mincgen - generate a MINC file from a CDL file
• mincheader - prints out complete header information for a minc file
• mincinfo - print out specified information about a minc file
• minclookup - perform lookup table conversions on minc files
• mincmakescalar - convert vector minc files to scalar
• mincmakevector - convert a list of scalar minc files into one vector file
• mincmath - perform simple math operations on minc files
• mincresample - resamples a minc file along new spatial dimensions
• mincreshape - cuts a hyperslab out of a minc file (with dimension re-ordering)
• mincsample - generate samplings from minc files
• mincstats - calculate simple statistics across voxels of a minc file
• minctoecat - convert a minc format file to an Ecat7 format file
• minctoraw - copy data from a MINC file
• mincview - view a MINC file
• mincwindow - limit voxel values to a given range
• mnc2nii - convert a MINC format file to a NIfTI-1 or Analyze format file
• mrisim - (no description available)
• mritoself - intra-subject registration of two volumetric data sets
• mritotal - performs multi-scale fitting of a normal human brain to a standard model
• nii2mnc - convert a NIfTI-1 or Analyze 7.5 format file to a MINC format file
• postf - a medical image display utility
• rawtominc - converts a stream of binary image data to a minc format file
• register - interactive volume display and point tagging program
• upet2mnc - convert a Concorde microPET format file to a MINC format file
• vff2mnc - convert set of vff file(s) to one 3D MINC2.0 format file
• voxeltoworld - convert voxel coordinates to world coordinates
• worldtovoxel - convert world coordinates to voxel coordinates
• xfm2def - convert a MNI transform file to a deformation volume
• xfmconcat - concatenate MNI transform files
• xfmflip - flip an MNI transform file
• xfminvert - invert an MNI transform file
• xdisp - an image display utility for the X Window System