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