Evaluate and ROI-oriented programs

peak_4dfp

locate and consolidate maxima to generate ROI

Usage: peak_4dfp <file_4dfp>

Examples:

peak_4dfp grand_average_222[.4dfp.img] -s10

Options

-s<flt> preblur with hard sphere kernel of specified radius (invokes hsphere_4dfp)
-n<int> limit initial pos and neg peak list lengths (default=1000)
-c<flt>[to<flt>] specify sign inverted curvature thresholds (default none)
-v<flt>[to<flt>] specify peak value thresholds (default none)
-d<flt> consolidate extremum pairs closer than specified distance
-o<flt> output a fidl compatible 4dfp format ROI file with regions of specified radius
-m<str> apply named mask file to output ROIs
-N<int> specify output ROI minimum voxel count (default = 1)
-a<str> append specified string to ROI output filename
-q quiet mode (suppress rec file listing)
-F force preblur image creation even if hsphere_4dfp result exists (no effect without -s<flt>)
-@<b|l> output big or little endian (default input endian)

N.B.: operations controlled by options -s, -n, -c, -v, -d, -o, -m, -N are applied serially in listed order
N.B.: all distances are in mm

read_4dfp

report value of image at specified real coordinate

Usage: read_4dfp <flt x0> <flt y0> <flt z0> <4dfp imgroot> [options]

Examples:

read_4dfp 33.1 -56.2 18. grand_average_222[.4dfp.img]

Options

-v verbose mode

imgmax_4dfp

report maximum and minimum values

Usage: imgmax_4dfp <my_image[.4dfp.img]>

Options

-m report min as well as max
-e report max/min values in scientific notation
-r report root sum of squares
-v verbose (time series) mode

img_hist_4dfp

construct voxel value histogram; evaluate moments

Usage: img_hist_4dfp <(4dfp) image>

Options

-b<int> specify number of bins (default = 100)
-f<int> select volume (counting from 1) of 4dfp stack (default analyze all volumes)
-t<flt> specify image intensity threshold
-r<flt>[to<flt>] specify histogram range
-m<(4dfp) mask> mask input using (non-zero voxels of) specified mask (only first frame used)
-h create <image>.hist file suitable for plotting, e.g., with xmgr
-p create <image>.dat file suitable for input to numerical procedures
-x create <image>.xtile percentile listing
-C create output files in $cwd (default parallel to <(4dfp) image>)
-u normalize output .hist and .dat distributions to unit area
-s report moments

N.B.: option -f causes selected volume to be reported in filename of -{hpx} created files

qnt_4dfp

report mean value within 3D ROI

Usage: qnt_4dfp <(4dfp)|(conc) image> <(4dfp) mask>

Examples:

qnt_4dfp -t23.2 va1234_mpr mask

Options

-s time series mode
-d include backwards differences (differentiated signal) in output (requires -f or -F, implies -s)
-D count only defined (finite, non 0.0, non-NaN, non 1.e-37) <image> voxels
-A apply threshold test to absolute value of <mask>
-W interpret <mask> as spatial weights (negative values allowed) (disables mask threshold testing)
-v<flt>[to<flt>] count only <image> voxels within specified range
-f<str> specify frames to count format, e.g., “4x120+4x76+”
-F<str> read frames-to-count format from specified file
-p<flt> specify mask threshold as percent of <mask> max
-t<flt> specify absolute <mask> threshold (default = 0.0)
-c<flt> scale output mean values by specified constant (default = 1.0)

N.B.: only the first frame of <mask> is used
N.B.: <image> and <mask> may be the same
N.B.: conc files must have extension “conc”

qntm_4dfp

evaluate multiple volumes in multiple ROIs

Usage: qntm_4dfp <(4dfp)|(conc) image> <(4dfp) ROI>

Examples:

qntm_4dfp TC30274_rmsp_faln_dbnd_xr3d_atl.conc iter10_roi_-02_-37_+27m_ROI

Options

-Z count zero voxels in <image> as defined
-V force code_by_volume even if the number of volumes is 1
-N create ROIs/voxel image
-o<str> write output to specified text file (default stdout)
-h suppress printing output header

N.B.: conc files must have extension “conc”
N.B.: only defined voxels (not 0.0 and not NaN and not 1.e-37 and finite) are counted
N.B.: <(4dfp) ROI> may either a value-coded single volume ROI image or a multi-volume mask
N.B.: <(4dfp) ROI> coded values are integerized
N.B.: qntm_4dfp ignores <(4dfp) ROI> ifh center and mmppix fields

qntv_4dfp

evaluate multiple volumes in ROI subdivided into cubes

Usage: qntv_4dfp <(4dfp)|(conc) image> <(4dfp) ROI>

Examples:

qntv_4dfp TC30274_rmsp_faln_dbnd_xr3d_atl.conc iter10_roi_-02_-37_+27m_ROI

Options

-H include header info in output
-V print defined voxel counts per die
-D create die image (voxels >= ncrit)
-K create die (voxel) coordinate listing
-Z count zero voxels in <image> as defined
-O<int> select output type (see below)
-f<str> specify frames-to-count format (default count all frames)
-F<str> read frames-to-count format from specified file (supersedes option -f)
-l<int> specify length of die in voxels (default 1)
-n<int> specify minimum die voxel count (default 1)
-t<flt> specify svd output tolerance - ratio of least to greatest eigenvalue (default 1e-06)
-o<str> write output to specified text file (default stdout)

-O<int> options

1 timeseries directly extracted from dice
2 timeseries extracted from dice with mean removed
3 die timeseries passed through svd multiplied by eigenvalue
4 die timeseries passed through svd (unit variance)

N.B.: conc files must have extension “conc”
N.B.: only defined voxels (not 0.0 and not NaN and not 1.e-37 and finite) are counted
N.B.: qntv_4dfp ignores <(4dfp) ROI> ifh center and mmppix fields
N.B.: to obtain a GLM condition number = X specificy sqrt(1/X) as tol with option -t

qntw_4dfp

evaluate multiple volumes using weighted ROI

Usage: qntw_4dfp <(4dfp)|(conc) image> <(4dfp) ROI>

Examples:

qntw_4dfp TC30274_rmsp_faln_dbnd_xr3d_atl.conc iter10_roi_-02_-37_+27m_ROI

Options

-L<int> specify ROI weight L-norm (default = 0)
-o<str> write output to specified text file (default stdout)
-Z count zero voxels in <image> as defined
-H include heaer info in output

N.B.: conc files must have extension “conc”
N.B.: <(4dfp) ROI> is interpreted as a multi-volume voxel-wise set of weights
N.B.: only defined voxels (not 0.0 and not NaN and not 1.e-37 and finite) are counted
N.B.: qntw_4dfp ignores <(4dfp) ROI> ifh center and mmppix fields

var_4dfp

evaluate variance or s.d. about mean over timeseries

Usage: var_4dfp <(4dfp|conc) input>

Examples:

var_4dfp -sn3 -c10 test_b1_rmsp_dbnd

Options

-d debug mode
-m remove mean volume from stack
-s compute s.d. about mean
-G compute mean ignoring run boundaries (default within runs)
-v compute variance about mean (default operation)
-z output logical and of all defined voxels
-n<int> specify number of pre-functional frames per run (default = 0)
-f<str> specify frames to count format, e.g., “4x120+4x76+” (overrides -n)
-F<str> read format from specified file
-c<flt> scale output image values by specified factor
-N output undefined voxels as NaN
-Z output undefined voxels as 0
-E output undefined voxels as 1.e-37 (default)
-@<b|l> output big or little endian (default input endian)

N.B.: input conc files must have extension “conc”
N.B.: identically zero input voxels are counted as defined
N.B.: options {-v -s -m -z} are mutually exclusive
N.B.: absent -G voxelwise mean is individually computed over each run in conc
N.B.: -f option overrides -n

dvar_4dfp

evaluate variance or s.d. about mean over differentiated timeseries

Usage: dvar_4dfp [options] <stack_4dfp>

Examples:

dvar_4dfp -n3 test_b1_rmsp_dbnd -mtest_anat_ave_mskt

Options

-m<(4dfp) mask> use specified 4dfp mask
-n<int> specify number of pre-functional (anatomy) frames
-t<flt> specify maskfile threshold (default = 0.0)
-b<flt> specify preblur FWHM in mm (default none)
-s output sqrt(dvar) (default dvar)
-@<b|l> output big or little endian (default input endian)

burn_sphere_4dfp

“burn in” sphere at specified real coordinates

Usage: burn_sphere_4dfp <flt x0> <flt y0> <flt z0> <4dfp imgroot> <4dfp outroot> [options]

Examples:

burn_sphere_4dfp 33.1 -56.2 18. grand_average_222[.4dfp.img] -v2 -o7.5
burn_sphere_4dfp 33.1 -56.2 18. 222 -v2 -o7.5

Options

-a superimpose sphere on image (default duplicate input format with zero background)
-s sum overlapping spheres (default overwrite)
-v<flt> specify burn in value (default=1.0000)
-o<flt> specify sphere radius in mm (default=6.0000) (radius of 0 creates single pixel burn)
-l<lst> read sphere coordinates from specified list (command line coords ignored)
-@<b|l> output big or little endian (default input endian)

N.B.: without -a only the input ifh (or standard atlas string) is required
N.B.: specifying <4dfp imgroot> as “333[.n]” “222” or “111” generates standard atlas space output
N.B.: if the 4dfp image does not exist the default output endianness is CPU endian

ROI_resolve_4dfp

resolve a set of possibly overlapping ROIs into a disjoint set

Usage: ROI_resolve_4dfp <(4dfp) ROI1> <(4dfp) ROI2> <(4dfp) ROI3> …

Options

-l<lst> read input file names from specified list file
-@<b|l> output big or little endian (default CPU endian)

N.B.: output 4dfp fileroots are same as inputs with appended “z”

imgsurf_4dfp

move ROI coordinates to nearest surface

Usage: imgsurf_4dfp <(4dfp) image> <point_list>

N.B.: <point_list> lists loci in atlas coordinates (X Y Z) in mm

spatial_corr_4dfp

compute image similarity as correlation over space

Usage: spatial_corr_4dfp <image_x> <mask_x> <image_y> <mask_y> [output_text_file]

Options

-C compute covariance (default correlation)
-M suppress removal of patial means
-c<flt> scale output covariance matrix values by specified factor

N.B.: image dimensions must match
N.B.: spatial_corr_4dfp counts only defined (not NaN or 1.e-37 or 0.0) voxels

spatial_cov_multivol_4dfp

compute volume-pair covariance over space

Usage: spatial_cov_multivol_4dfp <(4dfp) image> <(4dfp) mask>

Options

-Z compute covariance with respect to zero (default wrt image mean)
-p<int> generate specified number of PCs (default none)
-c<flt> scale text output covariance matrix values by specified factor

N.B.: spatial_cov_multivol_4dfp counts only defined (not NaN or 1.e-37) voxels
N.B.: zero voxels are counted as defined in <(4dfp) image> in cov computation
N.B.: zero voxels are counted as undefined in <(4dfp) image> in <(4dfp) mask>
N.B.: all zero or all undefined <(4dfp) image> volumes are ignored