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