【FSL/MRtrix】画像の切り取り・マスキング ~Masking~

Usage: fslmaths [-dt <datatype>] <first_input> [operations and inputs] <output> [-odt <datatype>]

Datatype information:
 -dt sets the datatype used internally for calculations (default float for all except double images)
 -odt sets the output datatype ( default is float )
 Possible datatypes are: char short int float double input
 "input" will set the datatype to that of the original image

Binary operations:
  (some inputs can be either an image or a number)
 -add   : add following input to current image
 -sub   : subtract following input from current image
 -mul   : multiply current image by following input
 -div   : divide current image by following input
 -rem   : modulus remainder - divide current image by following input and take remainder
 -mas   : use (following image>0) to mask current image
 -thr   : use following number to threshold current image (zero anything below the number)
 -thrp  : use following percentage (0-100) of ROBUST RANGE to threshold current image (zero anything below the number)
 -thrP  : use following percentage (0-100) of ROBUST RANGE of non-zero voxels and threshold below
 -uthr  : use following number to upper-threshold current image (zero anything above the number)
 -uthrp : use following percentage (0-100) of ROBUST RANGE to upper-threshold current image (zero anything above the number)
 -uthrP : use following percentage (0-100) of ROBUST RANGE of non-zero voxels and threshold above
 -max   : take maximum of following input and current image
 -min   : take minimum of following input and current image
 -seed  : seed random number generator with following number
 -restart : replace the current image with input for future processing operations
 -save : save the current working image to the input filename

Basic unary operations:
 -exp   : exponential
 -log   : natural logarithm
 -sin   : sine function
 -cos   : cosine function
 -tan   : tangent function
 -asin  : arc sine function
 -acos  : arc cosine function
 -atan  : arc tangent function
 -sqr   : square
 -sqrt  : square root
 -recip : reciprocal (1/current image)
 -abs   : absolute value
 -bin   : use (current image>0) to binarise
 -binv  : binarise and invert (binarisation and logical inversion)
 -fillh : fill holes in a binary mask (holes are internal - i.e. do not touch the edge of the FOV)
 -fillh26 : fill holes using 26 connectivity
 -index : replace each nonzero voxel with a unique (subject to wrapping) index number
 -grid <value> <spacing> : add a 3D grid of intensity <value> with grid spacing <spacing>
 -edge  : edge strength
 -tfce <H> <E> <connectivity>: enhance with TFCE, e.g. -tfce 2 0.5 6 (maybe change 6 to 26 for skeletons)
 -tfceS <H> <E> <connectivity> <X> <Y> <Z> <tfce_thresh>: show support area for voxel (X,Y,Z)
 -nan   : replace NaNs (improper numbers) with 0
 -nanm  : make NaN (improper number) mask with 1 for NaN voxels, 0 otherwise
 -rand  : add uniform noise (range 0:1)
 -randn : add Gaussian noise (mean=0 sigma=1)
 -inm <mean> :  (-i i ip.c) intensity normalisation (per 3D volume mean)
 -ing <mean> :  (-I i ip.c) intensity normalisation, global 4D mean)
 -range : set the output calmin/max to full data range

Matrix operations:
 -tensor_decomp : convert a 4D (6-timepoint )tensor image into L1,2,3,FA,MD,MO,V1,2,3 (remaining image in pipeline is FA)

Kernel operations (set BEFORE filtering operation if desired):
 -kernel 3D : 3x3x3 box centered on target voxel (set as default kernel)
 -kernel 2D : 3x3x1 box centered on target voxel
 -kernel box    <size>     : all voxels in a cube of width <size> mm centered on target voxel
 -kernel boxv   <size>     : all voxels in a cube of width <size> voxels centered on target voxel, CAUTION: size should be an odd number
 -kernel boxv3  <X> <Y> <Z>: all voxels in a cuboid of dimensions X x Y x Z centered on target voxel, CAUTION: size should be an odd number
 -kernel gauss  <sigma>    : gaussian kernel (sigma in mm, not voxels)
 -kernel sphere <size>     : all voxels in a sphere of radius <size> mm centered on target voxel
 -kernel file   <filename> : use external file as kernel

Spatial Filtering operations: N.B. all options apart from -s use the default kernel or that _previously_ specified by -kernel
 -dilM    : Mean Dilation of non-zero voxels
 -dilD    : Modal Dilation of non-zero voxels
 -dilF    : Maximum filtering of all voxels
 -dilall  : Apply -dilM repeatedly until the entire FOV is covered
 -ero     : Erode by zeroing non-zero voxels when zero voxels found in kernel
 -eroF    : Minimum filtering of all voxels
 -fmedian : Median Filtering 
 -fmean   : Mean filtering, kernel weighted (conventionally used with gauss kernel)
 -fmeanu  : Mean filtering, kernel weighted, un-normalised (gives edge effects)
 -s <sigma> : create a gauss kernel of sigma mm and perform mean filtering
 -subsamp2  : downsamples image by a factor of 2 (keeping new voxels centred on old)
 -subsamp2offc  : downsamples image by a factor of 2 (non-centred)

Dimensionality reduction operations:
  (the "T" can be replaced by X, Y or Z to collapse across a different dimension)
 -Tmean   : mean across time
 -Tstd    : standard deviation across time
 -Tmax    : max across time
 -Tmaxn   : time index of max across time
 -Tmin    : min across time
 -Tmedian : median across time
 -Tperc <percentage> : nth percentile (0-100) of FULL RANGE across time
 -Tar1    : temporal AR(1) coefficient (use -odt float and probably demean first)

Basic statistical operations:
 -pval    : Nonparametric uncorrected P-value, assuming timepoints are the permutations; first timepoint is actual (unpermuted) stats image
 -pval0   : Same as -pval, but treat zeros as missing data
 -cpval   : Same as -pval, but gives FWE corrected P-values
 -ztop    : Convert Z-stat to (uncorrected) P
 -ptoz    : Convert (uncorrected) P to Z
 -rank    : Convert data to ranks (over T dim)
 -ranknorm: Transform to Normal dist via ranks

Multi-argument operations:
 -roi <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> : zero outside roi (using voxel coordinates). Inputting -1 for a size will set it to the full image extent for that dimension.
 -bptf  <hp_sigma> <lp_sigma> : (-t in ip.c) Bandpass temporal filtering; nonlinear highpass and Gaussian linear lowpass (with sigmas in volumes, not seconds); set either sigma<0 to skip that filter
 -roc <AROC-thresh> <outfile> [4Dnoiseonly] <truth> : take (normally binary) truth and test current image in ROC analysis against truth. <AROC-thresh> is usually 0.05 and is limit of Area-under-ROC measure FP axis. <outfile> is a text file of the ROC curve (triplets of values: FP TP threshold). If the truth image contains negative voxels these get excluded from all calculations. If <AROC-thresh> is positive then the [4Dnoiseonly] option needs to be set, and the FP rate is determined from this noise-only data, and is set to be the fraction of timepoints where any FP (anywhere) is seen, as found in the noise-only 4d-dataset. This is then controlling the FWE rate. If <AROC-thresh> is negative the FP rate is calculated from the zero-value parts of the <truth> image, this time averaging voxelwise FP rate over all timepoints. In both cases the TP rate is the average fraction of truth=positive voxels correctly found.

Combining 4D and 3D images:
 If you apply a Binary operation (one that takes the current image and a new image together), when one is 3D and the other is 4D,
 the 3D image is cloned temporally to match the temporal dimensions of the 4D image.

e.g. fslmaths inputVolume -add inputVolume2 output_volume
     fslmaths inputVolume -add 2.5 output_volume
     fslmaths inputVolume -add 2.5 -mul inputVolume2 output_volume

     fslmaths 4D_inputVolume -Tmean -mul -1 -add 4D_inputVolume demeaned_4D_inputVolume

SYNOPSIS

     Apply generic voxel-wise mathematical operations to images

USAGE

     mrcalc [ options ] operand [ operand ... ]

        operand      an input image, intensity value, or the special keywords
                     'rand' (random number between 0 and 1) or 'randn' (random
                     number from unit std.dev. normal distribution) or the
                     mathematical constants 'e' and 'pi'.


DESCRIPTION

     This command will only compute per-voxel operations. Use 'mrmath' to
     compute summary statistics across images or along image axes.

     This command uses a stack-based syntax, with operators (specified using
     options) operating on the top-most entries (i.e. images or values) in the
     stack. Operands (values or images) are pushed onto the stack in the order
     they appear (as arguments) on the command-line, and operators (specified
     as options) operate on and consume the top-most entries in the stack, and
     push their output as a new entry on the stack.

     As an additional feature, this command will allow images with different
     dimensions to be processed, provided they satisfy the following
     conditions: for each axis, the dimensions match if they are the same size,
     or one of them has size one. In the latter case, the entire image will be
     replicated along that axis. This allows for example a 4D image of size [ X
     Y Z N ] to be added to a 3D image of size [ X Y Z ], as if it consisted of
     N copies of the 3D image along the 4th axis (the missing dimension is
     assumed to have size 1). Another example would a single-voxel 4D image of
     size [ 1 1 1 N ], multiplied by a 3D image of size [ X Y Z ], which would
     allow the creation of a 4D image where each volume consists of the 3D
     image scaled by the corresponding value for that volume in the
     single-voxel image.

EXAMPLE USAGES

     Double the value stored in every voxel:
       $ mrcalc a.mif 2 -mult r.mif
     This performs the operation: r = 2*a  for every voxel a,r in images a.mif
     and r.mif respectively.

     A more complex example:
       $ mrcalc a.mif -neg b.mif -div -exp 9.3 -mult r.mif
     This performs the operation: r = 9.3*exp(-a/b)

     Another complex example:
       $ mrcalc a.mif b.mif -add c.mif d.mif -mult 4.2 -add -div r.mif
     This performs: r = (a+b)/(c*d+4.2).

     Rescale the densities in a SH l=0 image:
       $ mrcalc ODF_CSF.mif 4 pi -mult -sqrt -div ODF_CSF_scaled.mif
     This applies the spherical harmonic basis scaling factor: 1.0/sqrt(4*pi),
     such that a single-tissue voxel containing the same intensities as the
     response function of that tissue should contain the value 1.0.

basic operations

  -abs  (multiple uses permitted)
     |%1| : return absolute value (magnitude) of real or complex number

  -neg  (multiple uses permitted)
     -%1 : negative value

  -add  (multiple uses permitted)
     (%1 + %2) : add values

  -subtract  (multiple uses permitted)
     (%1 - %2) : subtract nth operand from (n-1)th

  -multiply  (multiple uses permitted)
     (%1 * %2) : multiply values

  -divide  (multiple uses permitted)
     (%1 / %2) : divide (n-1)th operand by nth

  -min  (multiple uses permitted)
     min (%1, %2) : smallest of last two operands

  -max  (multiple uses permitted)
     max (%1, %2) : greatest of last two operands

comparison operators

  -lt  (multiple uses permitted)
     (%1 < %2) : less-than operator (true=1, false=0)

  -gt  (multiple uses permitted)
     (%1 > %2) : greater-than operator (true=1, false=0)

  -le  (multiple uses permitted)
     (%1 <= %2) : less-than-or-equal-to operator (true=1, false=0)

  -ge  (multiple uses permitted)
     (%1 >= %2) : greater-than-or-equal-to operator (true=1, false=0)

  -eq  (multiple uses permitted)
     (%1 == %2) : equal-to operator (true=1, false=0)

  -neq  (multiple uses permitted)
     (%1 != %2) : not-equal-to operator (true=1, false=0)

conditional operators

  -if  (multiple uses permitted)
     (%1 ? %2 : %3) : if first operand is true (non-zero), return second
     operand, otherwise return third operand

  -replace  (multiple uses permitted)
     (%1, %2 -> %3) : Wherever first operand is equal to the second operand,
     replace with third operand

power functions

  -sqrt  (multiple uses permitted)
     sqrt (%1) : square root

  -pow  (multiple uses permitted)
     %1^%2 : raise (n-1)th operand to nth power

nearest integer operations

  -round  (multiple uses permitted)
     round (%1) : round to nearest integer

  -ceil  (multiple uses permitted)
     ceil (%1) : round up to nearest integer

  -floor  (multiple uses permitted)
     floor (%1) : round down to nearest integer

logical operators

  -not  (multiple uses permitted)
     !%1 : NOT operator: true (1) if operand is false (i.e. zero)

  -and  (multiple uses permitted)
     (%1 && %2) : AND operator: true (1) if both operands are true (i.e.
     non-zero)

  -or  (multiple uses permitted)
     (%1 || %2) : OR operator: true (1) if either operand is true (i.e.
     non-zero)

  -xor  (multiple uses permitted)
     (%1 ^^ %2) : XOR operator: true (1) if only one of the operands is true
     (i.e. non-zero)

classification functions

  -isnan  (multiple uses permitted)
     isnan (%1) : true (1) if operand is not-a-number (NaN)

  -isinf  (multiple uses permitted)
     isinf (%1) : true (1) if operand is infinite (Inf)

  -finite  (multiple uses permitted)
     finite (%1) : true (1) if operand is finite (i.e. not NaN or Inf)

complex numbers

  -complex  (multiple uses permitted)
     (%1 + %2 i) : create complex number using the last two operands as
     real,imaginary components

  -polar  (multiple uses permitted)
     (%1 /_ %2) : create complex number using the last two operands as
     magnitude,phase components (phase in radians)

  -real  (multiple uses permitted)
     real (%1) : real part of complex number

  -imag  (multiple uses permitted)
     imag (%1) : imaginary part of complex number

  -phase  (multiple uses permitted)
     phase (%1) : phase of complex number (use -abs for magnitude)

  -conj  (multiple uses permitted)
     conj (%1) : complex conjugate

  -proj  (multiple uses permitted)
     proj (%1) : projection onto the Riemann sphere

exponential functions

  -exp  (multiple uses permitted)
     exp (%1) : exponential function

  -log  (multiple uses permitted)
     log (%1) : natural logarithm

  -log10  (multiple uses permitted)
     log10 (%1) : common logarithm

trigonometric functions

  -cos  (multiple uses permitted)
     cos (%1) : cosine

  -sin  (multiple uses permitted)
     sin (%1) : sine

  -tan  (multiple uses permitted)
     tan (%1) : tangent

  -acos  (multiple uses permitted)
     acos (%1) : inverse cosine

  -asin  (multiple uses permitted)
     asin (%1) : inverse sine

  -atan  (multiple uses permitted)
     atan (%1) : inverse tangent

hyperbolic functions

  -cosh  (multiple uses permitted)
     cosh (%1) : hyperbolic cosine

  -sinh  (multiple uses permitted)
     sinh (%1) : hyperbolic sine

  -tanh  (multiple uses permitted)
     tanh (%1) : hyperbolic tangent

  -acosh  (multiple uses permitted)
     acosh (%1) : inverse hyperbolic cosine

  -asinh  (multiple uses permitted)
     asinh (%1) : inverse hyperbolic sine

  -atanh  (multiple uses permitted)
     atanh (%1) : inverse hyperbolic tangent

Data type options

  -datatype spec
     specify output image data type. Valid choices are: float32, float32le,
     float32be, float64, float64le, float64be, int64, uint64, int64le,
     uint64le, int64be, uint64be, int32, uint32, int32le, uint32le, int32be,
     uint32be, int16, uint16, int16le, uint16le, int16be, uint16be, cfloat32,
     cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be, int8, uint8,
     bit.

Standard options

  -info
     display information messages.

  -quiet
     do not display information messages or progress status; alternatively,
     this can be achieved by setting the MRTRIX_QUIET environment variable to a
     non-empty string.

  -debug
     display debugging messages.

  -force
     force overwrite of output files (caution: using the same file as input and
     output might cause unexpected behaviour).

  -nthreads number
     use this number of threads in multi-threaded applications (set to 0 to
     disable multi-threading).

  -config key value  (multiple uses permitted)
     temporarily set the value of an MRtrix config file entry.

  -help
     display this information page and exit.

  -version
     display version information and exit.