conda install -c vfonov falcon - will work on linux
Prerequisites: minc-toolkit-v2 (http://bic-mni.github.io/), libtiff, povray, imagemagick
cmake <source_dir> \
-DCMAKE_INSTALL_PREFIX:PATH=<install prefix> \
-DMINC_TOOLKIT_DIR:PATH=/opt/minc/1.9.17 \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DHAVE_POVRAY:BOOL=ON \
-DUSE_OPENMP:BOOL=ON
make && make install
- falcon_run.sh - execute FALCON surface extraction pipeline
falcon_run.sh <input.mnc> <output_base> -brain <brain_mask.mnc>
parameters:
-help : show this usage
---- Required parameters ---
-brain <brain mask.mnc> : brain mask
--- Recomended parameters ---
-nl <nl.xfm> : nonlinear registration to icbm [default = None, will run ANTs]
-omp <omp> : change number of processors [default=1]
-use_icbm : use mesh from ICBM for initialization , default - use shrink-wrap
-anlm : apply anlm filter to input t1w scan (if not done before)
-postprocess : apply post-procesiing: resample mesh to atlas, calculate thickness
--- Optional parameters ---
-vent <vent.mnc> : ventricle mask [default = None]
-cerebellum <cerebellum.mnc> : cerebellum mask [default = None]
-brainstem <brainstem.mnc> : brainstem mask [default = None]
-cls <cls.mnc> : tissue classification map
-priors <WM> <GM> <CSF> : tissue priors, ( default: none )
-nopriors : don't use tissue priors, for surface fitting
--- Optional parameters (don't touch, if you don't know what you are doing) ---
-gwimask <mask.mnc> : gray matter - white matter interface mask [default = None]
-cerebellummask <mask.mnc> : cerebellum mask [default = None]
-wmmask <mask.mnc> : white matter mask [default = None]
-csfmask <csf.mnc> : CSF mask [default = None]
-left <left.mnc> : left hemisphere mask [default = None]
-right <right.mnc> : right hemisphere mask [default = None]
-sides <left.mnc> <right.mnc> : left and right hemisphere masks [default = None]
-variant <var> : for debugging
-trace : produce traces of intermediate surfaces
-hr : produce high-resolution thickness measurement in ICBM space
-smooth <fwhm> : smooth thickness maps (in addition)
-noremesh : don't remesh initial mesh (for DEBUGGING only)
-debug : run in debug mode (keep temp, echo commands)
-verbose : echo commands
- falcon_off_qc_2.sh - generate surface QC image for two hemispheres
falcon_off_qc_2.sh <input_lt.ply> <input_measurement_lt.csv> <input_rt.ply> <input_measurement_rt.csv> <output.png> [foreground] [background]
--- Optional parameters ---
-min <m> - minimal value for the measurement (default: minimum)
-max <m> - maximal value for the measurement (default: maximum)
-title <title> - plot title
-spectral - use spectral colour map (default)
-atrophy - use atrophy colour map
-summer - use summer colour map
-jacobian - use jacobian colour map
-gray - use gray colour map
-sphere - output on the spherical map, using spherical coordinates instead of x,y,z
-column <n> - specify column name from csv file to use (default will use the first column)
- falcon_off_qc.sh - generrate surface QC image for one hemisphere
falcon_off_qc.sh <input.off> <input_measurement.txt> <output.png> [foreground] [background]
--- Optional parameters ---
-min <m> - minimal value for the measurement (default: minimum)
-max <m> - maximal value for the measurement (default: maximum)
-title <title> - plot title
-spectral - use spectral colour map (default)
-atrophy - use atrophy colour map
-summer - use summer colour map
-jacobian - use jacobian colour map
-gray - use gray colour map
-sphere - output on the spherical map, using spherical coordinates instead of x,y,z
- falcon_slice_qc.sh - generate QC image showing intersection of surface and volume
falcon_slice_qc.sh <input.mnc> <ics.ply> <ocs.ply> <output.jpg/png/tiff>
--- Optional parameters ---
--min <f> - set image min (default: minimum)
--max <f> - set image max (default: maximum)
--pct <f> - set image max using percentile
- falcon_math - mathematical operations
-
primitive operations
- typeconvert -converts the image data type
- info -displays image stats
- infodiff -displays difference image stats
- infoabsdiff -displays absolute difference image stats
- clear -clears an image
- setone -sets one for an image
- setval -sets voxel value
- calcvol -calculates volumes
- labelvol -calculates volumes of label file
-
voxel-wise comparisons
- voxel-gt -greater than comparison
- voxel-ge -greater than or equal to comparison
- voxel-lt -less than comparison
- voxel-le -less than or equal to comparison
- voxel-eq -equal to comparison
- voxel-ne -not equal to comparison
-
arithmetic operations
- maskimg -mask image with a mask
- maskout -mask-out image with a mask
- resample -resamples image with new voxel spacing or image size
- avgimgs -average multiple images (voxel-by-voxel)
- mulimgs -multiply multiple images (voxel-by-voxel)
- maximgs -maximize multiple images (voxel-by-voxel)
- addimgs -add multiple images (voxel-by-voxel)
- subimg -subtract two images (voxel-by-voxel)
- absdiffimg -absolute difference of two images (voxel-by-voxel)
- divimg -subtract two images (voxel-by-voxel)
- ksub -subtract image voxel value from a constant
- heavisideF -heaviside function
- map-spectral -put spectral colors to an image
- map-jacobian -put jacobian colors to an image
- log -natural log
- avgimgs-fov -average multiple images with field-of-view correction
- kmul -multiply a constant (-val=)
- iscale -intensity scaling
- gaussPDF -gaussian normal PDF
- histo -creates histogram
- binimg -binarize image
- gaussnoise -image of Gaussian random
- fill-lesion -fill lesions as NAWM mean/stdv
- tiffimg -creates tiff of a slice
- bimodalfit -fits the intensity histogram to bimodal Gaussian distributions
- brainhistofit -fits intensity histogram to brain tissues (GM,WM,CSF)
- pseudoT2 -calculates T2 map from dual echo images
-
changing image size
- montage -image montage
- cropimg -crop image
- cropmask -crop image according to mask
- padimg -pads image with zeros
-
threshold operations
- thresh -threshold image
- otsu -threshold image using Otsu's algorithm
- ridler -threshold image using Ridler's algorithm
- maskthresh -threshold image and mask image (output is an image)
-
segmentation operations
- bseg -brain segmentation
- vseg -ventricle segmentation
- segcolor -write colored segmentation results
-
intensity normalization (and related functions)
- iscale -intensity scaling
- inorm -intensity normalization
- inorm2 -intensity normalization using histograms -registration is not required
- inorm3 -intensity normalization using linear regression -registration is required
- dbc -differential bias correction [Lewis and Fox 2004 NeuroImage]
-
boundary images
- bounds -creates a boundary image
- bounds-inc -creates a boundary image (boundary within mask)
- bounds-color -creates a boundary image with colors
-
create maps
- laplacemap -creates laplace map
- distancemap -creates signed distance map
- xdirimg -x-directional map (voxel intensity for voxel position)
- ydirimg -y-directional map (voxel intensity for voxel position)
- zdirimg -z-directional map (voxel intensity for voxel position)
- adirimg -directional maps (voxel intensity for voxel position, 3D)
-
image permutation
- permute-norm -converts to more or less RAS directions
- permute-left -turns left [x'=-y; y'=x; z'=z]
- permute-right -turns right [x'=y; y'=-x; z'=z]
- permute-cor2sag -rotates [x'=z; y'=y; z'=x]
- permute-cor2axi -rotates [x'=x; y'=z; z'=y]
- permute-sag2cor -rotates [x'=z; y'=z; z'=x]
- permute-sag2axi -rotates [x'=y; y'=z; z'=x]
- permute-cor2axi -rotates [x'=x; y'=z; z'=y]
- permute-axi2sag -rotates [x'=y; y'=z; z'=x]
- permute-axi2cor -rotates [x'=x; y'=z; z'=y]
- permute-flipxyz -flips in all x,y,z directions [x'=-x; y'=-y; z'=-z]
-
morphologic operations -uses -radius= to set the kernel radius
- open -morphologic opening
- close -morphologic closing
- dilate -morphologic dilation
- erode -morphologic erosion
- closeholes -morphologic closing by seed-filling background from image edge
- closebrain -series of morphologic operations to find brain ROI: (1) dilation, (2) close holes, and (3) erosion
-
simple filters
- gauss -gaussian filter
- median -median filter
- sobelx -x-directional sobel filter
- sobely -y-directional sobel filter
- sobelz -z-directional sobel filter
- sobelm -sobel filter magnitude sqrt(x^2+y^2+z^2)
- sobel -sobel filter for all directions
- sobelvoxel -sobel filter for a voxel
-
more than 3 dimensions -v (6th)-dimension is used as color in this set of programs
- mergetdim -merges images in t(4th)-dim
- mergeudim -merges images in u(5th)-dim
-
swap routines assume the largest dimension is unused
- swaput -swaps u and t dimensions
- swapuv -swaps u and v dimensions
- swapvt -swaps v and t dimensions
-
changing header info
- qformradio -puts arbitrary qform with center in middle
- removesqform -removes sform and qform
- copysqform -copies sform and qform to output image
- addsform -adds sform to an image
- modify-header-scl_slope -changes scl_slope
- modify-header-dz -changes dz
-
matrix operations
- invmatrix -inverts matrix
- multiplymatrix -multiplies (multiple) matrix(matrices)
- affine-decompose decompose-affine -decomposes matrix into affine parameters
- affinematrix -creates affine matrix
- halfway-matrix -calculates halfway matrix
- avgmatrix -calculates average of matrices (approximate)
- determinant -calculates determinant of a matrix
-
affine registration / transformation
- aregmni -affine registration to MNI152 in FSL
- aregmni-sform -affine registration to MNI152 in FSL -output matrix is put into image header sform
- applysform -applies affine transformation using sform
- writesform -writes sform affine transformation
- NBCSR -non-brain constrained symmetric registration
- NBCR -non-brain constrained registration (non-symmetric)
- NBCSR-rigid -non-brain constrained symmetric registration rigid (6-dof) version
- applyaffine -applies affine transformation using input matrix
- aregimg -affine registration
- aregimg2 -multi-seed/multi-resolution affine registration
-
nonlinear registration / transformation
- applywarp -nonlinearly transforms images
- nregimg -nonlinearly registers images (under construction)
- intratemplate -nonlinearly registers images from the same subject and create a template
-
OFF object processing
- cuberille -creates a surface model from a binary image
- applyaffine-obj -applies affine transformation using input
-
matrix on an off object - fsasc2off -converts FreeSurfer's ASCII format to off object
- shrinkwrap -shrink-wraps a mask image (not well validated)
- sphere-off -creates a sphere
- obj2img -creates boundary at the object surface
- avgobjs -averages objects, same object config required
- obj2pts off2pts -creates point file with a list of 3d coordinates for each vertex
- make-offe -write complete off file with offe file
- combine-obj -combine multiple off files
- add-off-color
- add-obj-color -adds one color to an object
- add-off-color-curvature
- add-obj-color-curvature -adds colors to an object based on curvatures
- add-off-color-sphere-theta -creates a color-map of spherical coordinates (theta)
- add-off-color-sphere-psi -creates a color-map of spherical coordinates (psi)
- offinfo -displays off information
- vertexinfo -displays vertex information
- edgeinfo -displays edge information
- faceinfo -displays face information
-
Cortex object processing (niikcortex)
-
niikcortex-initocs - creates initial pial surface
-
niikcortex-thick-color -assigns colour according to the cortical thickness -objlist=<white.off>,<pial.off> -out=<out_white.off>,<out_pial.off> -omin= minimum thickness for color range [default=auto] -omax= maximum thickness for color range [default=auto]
-
-
inter-packet (interleave) processing
- interpacket-correction -corrects interpacket patient motion by registering
- interpacket-split -splits interpacket (interleave) images by specified number
- interpacket-merge -merges interpacket (interleave) images
-
Other (less common)operations:
- grid-lines -creates image with grid-lines e.g. to show nonlinear deformation fields
- offinfo
-
general optional usage
- -u -help -help and general usage
- --version -version info
- -list -list of operations
-
common options
- -in=<img.nii> -set input image
- -out= -set output filename
- -obj=<obj.off> -set input object filename
- -imglist=<in1.nii>,<in2.nii>,... -list of input images
-
matrix options The matrix format is same as FSL The matrix is in ascii format and should not have empty rows
- -matrix= -set input matrix
- -matrixlist=,,...
-
-list of of input matrices -
-separate by comma - -invmatrix= -set and use inverse of input matrix
-
XFM options The transformation format is linear MINC XFM with single transform
- -xfm=<trans.xfm> -set input matrix
- -invxfm=<trans.xfm> -set and use inverse of input matrix
-
interpolation options
- -nn -nearest neighbor
- -linear -trilinear
- -bspline -b-spline
-
data types
- -uint8 -unsigned 8-bit integer
- -uint16 -unsigned 16-bit integer
- -uint32 -unsigned 32-bit integer
- -uint64 -unsigned 64-bit integer
- -int8 -8-bit signed integer
- -int16 -16-bit signed integer
- -int32 -32-bit signed integer
- -int64 -64-bit signed integer
- -float32 -32-bit floating point
- -float64 -64-bit floating point
-
- falcon_cortex_shrinkwrap - create initial surface, starting from a sphere using fast marching shrink-wrap algorithm
- falcon_cortex_initics - create initial inner surface , from an initial one
- falcon_cortex_initocs - create initial outer surface by expanding inner surface
- falcon_cortex_check_off - check two surfaces self-intersections and correct it
- falcon_cortex_refine - refine inner and outer mesh simultaneously
- falcon_cortex_calc_thickness - calculate distance between two meshes
- falcon_cortex_smooth - smooth two surfaces simultaneously
- falcon_cortex_measure - calculate surface parameters (mostly for debugging)
- falcon_surface_check - check surface for self-intersections
- falcon_surface_refine - modify surface
- falcon_surface_colour - colorize surface using measurements from another file
- falcon_surface_signals - extrace values along the surface from a volume
- falcon_surface_split - split surface into disconnected components
- falcon_transform_surface - apply transformation (.xfm file) - to a surface
- falcon_field_smooth - apply blurring along the surface
- falcon_obj2off - convert MNI .obj to .off or .ply file
- falcon_off2asc - convert .off or .ply file to .asc file
- falcon_off2ply - convert .off to .ply file
- falcon_ply2off - convert .ply to .off
- falcon_slice_extract - extract slices from a 3D volume with intersection lines from surfaces
- falcon_midsag - split white matter mask into hemishpheres
- Verbosity (and generation of debug files) is controlled by environment variable
FALCON_VERBOSE, set to integer to specify verbosity level, default is 0 - Prefix fox post-mortem files:
FALCON_POSTMORTEM_PREFIX - Location of debugging files (prefix):
FALCON_DEBUG_PREFIX - Base of FALCON installation:
FALCON_HOME, default useMINC_TOOLKIT - FALCON binaries:
FALCON_BIN, default :${FALCON_HOME}/bin - FALCON data:
FALCON_DATA, default :${FALCON_HOME}/share/falcon - FALCON scripts:
FALCON_SCRIPTS, default:${FALCON_HOME}/bin - If OpenMP is used,
OMP_NUM_THREADSspecifies maximum number of concurrent threads, default is number of CPU cores