Rearrange voxels in space or time
collate_slice_4dfp
collate interleaved datasets
Usage: collate_slice_4dfp <4dfp img1> <4dfp img2> … <4dfp imgn> <4dfp imgout>
Options
-v |
verbose mode |
-@<b|l> |
output big or little endian (default CPU endian) |
paste_4dfp
append or average selected frames from multiple files (list directed)
Usage: paste_4dfp <inlist> <outfile>
inlist is a file containing rows of 1 to 3 columns: filename, starting frame (counting from 1), number of frames.
Note
If a starting frame (column 2) is not specified, the first frame will be used.
Column 3 is only applied during append mode (-a). The period value (-p) will be used otherwise.
In append mode, column 3 has priority over the -p flag. The period value (-p) will only be used for rows that do not specify column 3.
Options
-a |
append successive epochs (default average) |
-p<int> |
specify period in frames (default=1) |
-@<b|l> |
output big or little endian (default initial input endian) |
extract_frame_4dfp
extract single frame from stack (paste_4dfp wrapper)
Usage: extract_frame_4dfp <(4dfp) stack> <(int) frame>
Examples:
extract_frame_4dfp CDR.5to1+ 3
Options
-o<str> |
specifiy output 4dfp fileroot (default = <stack>_frame<frame>) |
chop_4dfp
extract contiguous frames from stack (paste_4dfp wrapper)
usage: chop_4dfp <(4dfp) stack> <(int) frame0> <(int) frame1>
Examples:
chop_4dfp vb12345_b5_dbnd_xr3d[.4dfp[.img]] 4 68
Options
-o<str> |
specify output 4dfp fileroot (default = <stack>_frames<frame0>to<frame1>) |
crop_4dfp
crop or roll (correct image wrap)
Usage: crop_4dfp <(4dfp) inroot> [(4dfp) outroot]
Options
-<x|y|z><int>[to[<int>] |
specify x y z crop/expand limits (1-indexed) |
-s<x|y|z><int> |
scroll specified axis by specified number of pixels (after cropping/expanding) |
-f |
interpret specifications under 4dfp<->analyze flips |
-Z |
zero voxels instead of physically cropping |
-@<b|l> |
output big or little endian (default input endian) |
N.B.: if upper crop limit exceeds input dimension undefined voxels will be set to 1.e-37 N.B.: default (4dfp) output root is <(4dfp) inroot>”_crop”
reindex_4dfp
xy, slicevolume
Usage: reindex_4dfp <(4dfp> input> <index1> <index2> [options]
Examples:
reindex_4dfp my4Dstack 3 4
Options
-v |
verbose mode |
-o<str> |
specify 4dfp output root (default = <input>_r<index1><index2>) |
-@<b|l> |
output big or little endian (default input endian) |
N.B.: reindex_4dfp swaps specified indices N.B.: <index1> and <index2> must be unequal integers in the range 1-4 except as follows: <index1> == 4 and <index2> == 0: right rotate indices (first index <- last index) <index1> == 0 and <index2> == 4: left rotate indices ( last index <- first index)
unpack_4dfp
mosaic \(\rightarrow\) volume
Usage: unpack_4dfp <(4dfp) input> <(4dfp) output>
Examples:
unpack_4dfp 030211_EL_b_1 030211_EL_b1
Options
-V |
read frame count from input ifh slice count |
-R |
multiply output x and y voxsiz by pack factor |
-z |
flipz (unpack slices in reverse order) |
-y |
flipy |
-nx<int> |
specify unpacked nx (default=64) |
-ny<int> |
specify unpacked ny (default=64) |
-sx<int> |
squeeze unpacked x dimension by specified factor |
-sy<int> |
squeeze unpacked y dimension by specified factor |
-@<b|l> |
output big or little endian (default input endian) |
multipack_4dfp
volume \(\rightarrow\) mosaic
flip_4dfp
flip x, y, z
Usage: flip_4dfp <(4dfp) image> [(4dfp) output]
Examples:
flip_4dfp -yz vc345 vc345_flipyz
Options
-x |
flip x |
-y |
flip y |
-z |
flip z |
-@<b|l> |
output big or little endian (default input endian) |
N.B.: default output fileroot = <image>_flip[xyz]
split_4dfp
split assembled volumes
T2S_4dfp
transverse \(\rightarrow\) sagittal
Usage: T2S_4dfp <(4dfp) imgroot> [(4dfp) outroot]
- Examples::
T2S_4dfp vm6c_mpr T2S_4dfp vm6c_mpr vm6c_mprS
Options
-@<b|l> |
output big or little endian (default input endian) |
N.B.: default output root = <imgroot>”S”
S2T_4dfp
sagittal \(\rightarrow\) transverse
Usage: S2T_4dfp <(4dfp) imgroot> [(4dfp) outroot]
Examples:
S2T_4dfp vm6c_mpr
S2T_4dfp vm6c_mpr vm6c_mprT
Options
-@<b|l> |
output big or little endian (default input endian) |
N.B.: default output root = <imgroot>”T”
C2T_4dfp
coronal \(\rightarrow\) transverse
Usage: C2T_4dfp <(4dfp) image> [(4dfp) outroot]
Examples:
C2T_4dfp vm6c_b1
C2T_4dfp vm6c_b1 vm6c_b1T
Options
-@<b|l> |
output big or little endian (default input endian) |
N.B.: default output root = <imgroot>”T”
T2C_4dfp
transverse \(\rightarrow\) coronal
Usage: T2C_4dfp <(4dfp) imgroot> [(4dfp) outroot]
Examples:
T2C_4dfp vc12345_b1
T2C_4dfp vc12345_b1 vc12345_b1C
Options
-@<b|l> |
output big or little endian (default input endian) |
N.B.: default output root = <imgroot>”C”