Threshold and mask

zero_slice_4dfp

zero specified range of slices in selected direction

Usage: zero_slice_4dfp <4dfp image>

Examples:

zero_slice_4dfp vce20_mpr -z1to3
zero_slice_4dfp vce20_mpr <x|y|z> istart iend [outroot]

Options

-<x|y|z><int>to<int> specify x y z limits (single required argument mode)
-f interpret slice numbers using 4dfp<->analyze flips
-o specify output fileroot (default = <image>z)
-@<b|l> output big or little endian (default input endian)

N.B.: slices count from 1
N.B.: two usages are supported: 1 or 4 required arguments

zero_lt_4dfp

threshold by voxel value

Usage: zero_lt_4dfp <flt> <file_4dfp> [outroot]

Examples:

zero_lt_4dfp 90 pt349_study9to9
zero_lt_4dfp 90 pt349_study9to9 pt349_study9to9z

Options

-@<b|l> output big or little endian (default input endian)

N.B.: default output 4dfp root is <file_4dfp>”z”

zero_gt_4dfp

threshold by voxel value

Usage: zero_gt_4dfp <flt> <(4dfp) image> [outroot] [options]

Examples:

zero_gt_4dfp 90 pt349_study9to9
zero_gt_4dfp 90 pt349_study9to9 pt349_study9to9z

Options

-@<b|l> output big or little endian (default input endian)

N.B.: default output 4dfp root is <(4dfp) image>”z”
N.B.: first field can’t be used for options because threshold might be negative

zero_ltgt_4dfp

zero voxels outside specified range

Usage: zero_ltgt_4dfp <flt[to<flt>]> <(4dfp) image> [outroot] [options]

Examples:

zero_ltgt_4dfp -30to90 pt349_study9to9

Options

-@<b|l> output big or little endian (default input endian)

N.B.: default output 4dfp root is <(4dfp) image>”z”
N.B.: first field can’t be used for options because lower range might be negative

zero_gtlt_4dfp

zero voxels within specified range

Usage: zero_gtlt_4dfp <flt[to<flt>]> <(4dfp) image> [outroot] [options]

Examples:

zero_gtlt_4dfp -30to90 pt349_study9to9

Options

-@<b|l> output big or little endian (default input endian)

N.B.: default output 4dfp root is <(4dfp) image>”z”
N.B.: first field can’t be used for options because lower range might be negative

maskimg_4dfp

apply 4dfp mask to 4dfp image

Usage: maskimg_4dfp <(4dfp) imgfile> <(4dfp) mskfile> <(4dfp) outfile>

Examples:

maskimg_4dfp -t23.2 va1234_mpr mask va1234_mpr_msk

Options

-N replace NaN in <imgfile> with corresponding <mskfile> value
-e report to stdout mean <imgfile> within-mask value
-1 apply first frame of <mskfile> to all frames of <imgfile>
-R suppress creation of rec file
-v<flt> specify <outfile> uniform within-mask value
-p<flt> specify <mskfile> threshold as percent of <mskfile> max
-t<flt> specify <mskfile> threshold directly (default = 0.0)
-A threshold mask by absolute value of <mskfile>
-@<b|l> output big or little endian (default <imgfile> endian)

N.B.: <imgfile> and <mskfile> may be the same

cluster_4dfp

sort/count/zero (above threshold) contiguous voxels into clusters

Usage: cluster_4dfp <(4dfp) root>

Examples:

cluster_4dfp my_timage -At3.5

Options

-n<int> zero out clusters with voxel count below specified criterion (output image trailer = ‘clus’)
-f<int> address specified volume (counting from 1) of multi-volume stack (default is first volume)
-t<flt> specify image value threshold (default = 0)
-a<str> append specified string (preceded by “_”) to all output filenames
-@<b|l> output big or little endian (default input endian)
-A apply threshold test to image absolute value
-R convert clusters to (fidl compliant) ROI image (output image trailer = ‘ROI’)
-l create list file of region center of mass indices
-v verbose mode

N.B.: -l center of mass indices can be converted to atlas coordinates using index2atl -af