K-Lab

Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
       fslroi <input> <output> <tmin> <tsize>

       fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>
Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.

SYNOPSIS

     Perform conversion between different file types and optionally extract a
     subset of the input image

USAGE

     mrconvert [ options ] input output

        input        the input image.

        output       the output image.


DESCRIPTION

     If used correctly, this program can be a very useful workhorse. In
     addition to converting images between different formats, it can be used to
     extract specific studies from a data set, extract a specific region of
     interest, or flip the images. Some of the possible operations are
     described in more detail below.

     Note that for both the -coord and -axes options, indexing starts from 0
     rather than 1. E.g. -coord 3 <#> selects volumes (the fourth dimension)
     from the series; -axes 0,1,2 includes only the three spatial axes in the
     output image.

     Additionally, for the second input to the -coord option and the -axes
     option, you can use any valid number sequence in the selection, as well as
     the 'end' keyword (see the main documentation for details); this can be
     particularly useful to select multiple coordinates.

     The -vox option is used to change the size of the voxels in the output
     image as reported in the image header; note however that this does not
     re-sample the image based on a new voxel size (that is done using the
     mrresize command).

     By default, the intensity scaling parameters in the input image header are
     passed through to the output image header when writing to an integer
     image, and reset to 0,1 (i.e. no scaling) for floating-point and binary
     images. Note that the -scaling option will therefore have no effect for
     floating-point or binary output images.

     The -axes option specifies which axes from the input image will be used to
     form the output image. This allows the permutation, omission, or addition
     of axes into the output image. The axes should be supplied as a
     comma-separated list of axis indices. If an axis from the input image is
     to be omitted from the output image, it must either already have a size of
     1, or a single coordinate along that axis must be selected by the user by
     using the -coord option. Examples are provided further below.

     The -bvalue_scaling option controls an aspect of the import of diffusion
     gradient tables. When the input diffusion-weighting direction vectors have
     norms that differ substantially from unity, the b-values will be scaled by
     the square of their corresponding vector norm (this is how multi-shell
     acquisitions are frequently achieved on scanner platforms). However in
     some rare instances, the b-values may be correct, despite the vectors not
     being of unit norm (or conversely, the b-values may need to be rescaled
     even though the vectors are close to unit norm). This option allows the
     user to control this operation and override MRrtix3's automatic detection.

EXAMPLE USAGES

     Extract the first volume from a 4D image, and make the output a 3D image:
       $ mrconvert in.mif -coord 3 0 -axes 0,1,2 out.mif
     The -coord 3 0 option extracts, from axis number 3 (which is the fourth
     axis since counting begins from 0; this is the axis that steps across
     image volumes), only coordinate number 0 (i.e. the first volume). The
     -axes 0,1,2 ensures that only the first three axes (i.e. the spatial axes)
     are retained; if this option were not used in this example, then image
     out.mif would be a 4D image, but it would only consist of a single volume,
     and mrinfo would report its size along the fourth axis as 1.

     Extract slice number 24 along the AP direction:
       $ mrconvert volume.mif slice.mif -coord 1 24
     MRtrix3 uses a RAS (Right-Anterior-Superior) axis convention, and
     internally reorients images upon loading in order to conform to this as
     far as possible. So for non-exotic data, axis 1 should correspond
     (approximately) to the anterior-posterior direction.

     Extract only every other volume from a 4D image:
       $ mrconvert all.mif every_other.mif -coord 3 1:2:end
     This example demonstrates two features: Use of the colon syntax to
     conveniently specify a number sequence (in the format 'start:step:stop');
     and use of the 'end' keyword to generate this sequence up to the size of
     the input image along that axis (i.e. the number of volumes).

     Alter the image header to report a new isotropic voxel size:
       $ mrconvert in.mif isotropic.mif -vox 1.25
     By providing a single value to the -vox option only, the specified value
     is used to set the voxel size in mm for all three spatial axes in the
     output image.

     Alter the image header to report a new anisotropic voxel size:
       $ mrconvert in.mif anisotropic.mif -vox 1,,3.5
     This example will change the reported voxel size along the first and third
     axes (ideally left-right and inferior-superior) to 1.0mm and 3.5mm
     respectively, and leave the voxel size along the second axis (ideally
     anterior-posterior) unchanged.

     Turn a single-volume 4D image into a 3D image:
       $ mrconvert 4D.mif 3D.mif -axes 0,1,2
     Sometimes in the process of extracting or calculating a single 3D volume
     from a 4D image series, the size of the image reported by mrinfo will be
     "X x Y x Z x 1", indicating that the resulting image is in fact also 4D,
     it just happens to contain only one volume. This example demonstrates how
     to convert this into a genuine 3D image (i.e. mrinfo will report the size
     as "X x Y x Z".

     Insert an axis of size 1 into the image:
       $ mrconvert XYZD.mif XYZ1D.mif -axes 0,1,2,-1,3
     This example uses the value -1 as a flag to indicate to mrconvert where a
     new axis of unity size is to be inserted. In this particular example, the
     input image has four axes: the spatial axes X, Y and Z, and some form of
     data D is stored across the fourth axis (i.e. volumes). Due to insertion
     of a new axis, the output image is 5D: the three spatial axes (XYZ), a
     single volume (the size of the output image along the fourth axis will be
     1), and data D will be stored as volume groups along the fifth axis of the
     image.

     Manually reset the data scaling parameters stored within the image header
     to defaults:
       $ mrconvert with_scaling.mif without_scaling.mif -scaling 0.0,1.0
     This command-line option alters the parameters stored within the image
     header that provide a linear mapping from raw intensity values stored in
     the image data to some other scale. Where the raw data stored in a
     particular voxel is I, the value within that voxel is interpreted as:
     value = offset + (scale x I).  To adjust this scaling, the relevant
     parameters must be provided as a comma-separated 2-vector of
     floating-point values, in the format "offset,scale" (no quotation marks).
     This particular example sets the offset to zero and the scale to one,
     which equates to no rescaling of the raw intensity data.

Options for manipulating fundamental image properties

  -coord axis selection  (multiple uses permitted)
     retain data from the input image only at the coordinates specified in the
     selection along the specified axis. The selection argument expects a
     number sequence, which can also include the 'end' keyword.

  -vox sizes
     change the voxel dimensions reported in the output image header

  -axes axes
     specify the axes from the input image that will be used to form the output
     image

  -scaling values
     specify the data scaling parameters used to rescale the intensity values

Options for handling JSON (JavaScript Object Notation) files

  -json_import file
     import data from a JSON file into header key-value pairs

  -json_export file
     export data from an image header key-value pairs into a JSON file

Options to modify generic header entries

  -clear_property key  (multiple uses permitted)
     remove the specified key from the image header altogether.

  -set_property key value  (multiple uses permitted)
     set the value of the specified key in the image header.

  -append_property key value  (multiple uses permitted)
     append the given value to the specified key in the image header (this adds
     the value specified as a new line in the header value).

  -copy_properties source
     clear all generic properties and replace with the properties from the
     image / file specified.

Stride options

  -strides spec
     specify the strides of the output data in memory; either as a
     comma-separated list of (signed) integers, or as a template image from
     which the strides shall be extracted and used. The actual strides produced
     will depend on whether the output image format can support it.

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.

DW gradient table import options

  -grad file
     Provide the diffusion-weighted gradient scheme used in the acquisition in
     a text file. This should be supplied as a 4xN text file with each line is
     in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the
     applied gradient, and b gives the b-value in units of s/mm^2. If a
     diffusion gradient scheme is present in the input image header, the data
     provided with this option will be instead used.

  -fslgrad bvecs bvals
     Provide the diffusion-weighted gradient scheme used in the acquisition in
     FSL bvecs/bvals format files. If a diffusion gradient scheme is present in
     the input image header, the data provided with this option will be instead
     used.

  -bvalue_scaling mode
     enable or disable scaling of diffusion b-values by the square of the
     corresponding DW gradient norm (see Desciption). Valid choices are yes/no,
     true/false, 0/1 (default: automatic).

DW gradient table export options

  -export_grad_mrtrix path
     export the diffusion-weighted gradient table to file in MRtrix format

  -export_grad_fsl bvecs_path bvals_path
     export the diffusion-weighted gradient table to files in FSL (bvecs /
     bvals) format

Options for importing phase-encode tables

  -import_pe_table file
     import a phase-encoding table from file

  -import_pe_eddy config indices
     import phase-encoding information from an EDDY-style config / index file
     pair

Options for exporting phase-encode tables

  -export_pe_table file
     export phase-encoding table to file

  -export_pe_eddy config indices
     export phase-encoding information to an EDDY-style config / index file
     pair

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.

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.

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

USAGE

     mrthreshold [ options ] input [ output ]

        input        the input image to be thresholded

        output       the (optional) output binary image mask


DESCRIPTION

     The threshold value to be applied can be determined in one of a number of
     ways:

     - If no relevant command-line option is used, the command will
     automatically determine an optimal threshold;

     - The -abs option provides the threshold value explicitly;

     - The -percentile, -top and -bottom options enable more fine-grained
     control over how the threshold value is determined.

     The -mask option only influences those image values that contribute toward
     the determination of the threshold value; once the threshold is
     determined, it is applied to the entire image, irrespective of use of the
     -mask option. If you wish for the voxels outside of the specified mask to
     additionally be excluded from the output mask, this can be achieved by
     providing the -out_masked option.

     The four operators available through the "-comparison" option ("lt", "le",
     "ge" and "gt") correspond to "less-than" (<), "less-than-or-equal" (<=),
     "greater-than-or-equal" (>=) and "greater-than" (>). This offers
     fine-grained control over how the thresholding operation will behave in
     the presence of values equivalent to the threshold. By default, the
     command will select voxels with values greater than or equal to the
     determined threshold ("ge"); unless the -bottom option is used, in which
     case after a threshold is determined from the relevant lowest-valued image
     voxels, those voxels with values less than or equal to that threshold
     ("le") are selected. This provides more fine-grained control than the
     -invert option; the latter is provided for backwards compatibility, but is
     equivalent to selection of the opposite comparison within this selection.

     If no output image path is specified, the command will instead write to
     standard output the determined threshold value.

Threshold determination mechanisms

  -abs value
     specify threshold value as absolute intensity

  -percentile value
     determine threshold based on some percentile of the image intensity
     distribution

  -top count
     determine threshold that will result in selection of some number of
     top-valued voxels

  -bottom count
     determine & apply threshold resulting in selection of some number of
     bottom-valued voxels (note: implies threshold application operator of "le"
     unless otherwise specified)

Threshold determination modifiers

  -allvolumes
     compute a single threshold for all image volumes, rather than an
     individual threshold per volume

  -ignorezero
     ignore zero-valued input values during threshold determination

  -mask image
     compute the threshold based only on values within an input mask image

Threshold application modifiers

  -comparison choice
     comparison operator to use when applying the threshold; options are:
     lt,le,ge,gt (default = "le" for -bottom; "ge" otherwise)

  -invert
     invert the output binary mask (equivalent to flipping the operator;
     provided for backwards compatibility)

  -out_masked
     mask the output image based on the provided input mask image

  -nan
     set voxels that fail the threshold to NaN rather than zero (output image
     will be floating-point rather than binary)

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.