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

xy, slicevolume

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”