MINCMORPH(1)

💖 MINCMORPH(1) 💖

okay bestie, sit down, hydrate, because we're talking about mincmorph — it's one of the MNI medical image format tools and it is literally the moment. ✨

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🌸 SYNOPSIS 🌸

mincmorph [options] <in.mnc> <out.mnc>

like... you give it a file, you give it a name for the new file, you give it opinions. that's the whole vibe. 🫶

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🦋 DESCRIPTION 🦋

Command-specific options and general options, both living here rent free. Let's go.

✨ General Options ✨

• -verbose — be verbose. she talks. she tells you things. 🗣️
• -clobber — clobber existing files. yes, clobber. she will simply run over whatever's already there, no cap. 💀

🎀 Outfile Options 🎀

• -filetype — use the data type of the input file. matchy-matchy, we love that for her.
• -byte — write out byte data.
• -short — write out short integer data. (Default) 👑
• -int — write out long integer data.
• -float — write out single-precision data.
• -double — write out double-precision data.
• -signed — write signed integer data.
• -unsigned — write unsigned integer data.

🌈 Kernel Options 🌈

• -2D04 — use a 2D 4-connectivity kernel.
• -2D08 — use a 2D 8-connectivity kernel.
• -3D06 — use a 3D 6-connectivity kernel. (default) 👑
• -3D26 — use a 3D 26-connectivity kernel.
• -kernel — <kernel.kern> read in a custom kernel file. bring your own kernel, main character energy. 💅

🧚 Morphology Options 🧚

• -floor — the lower value for binarising or clamping. Default value: -1.79769e+308
• -ceil — upper value for binarising or clamping (incl). Default value: 1.79769e+308
• -range — range for binarising or clamping (incl). Default value: -1.79769e+308 1.79769e+308
• -foreground — foreground value. Default value: 1
• -background — background value. Default value: 0

💫 Single morphological operations 💫

• -binarise — binarise volume using the input range.
• -clamp — clamp volume using the input range.
• -pad — pad volume with respect to the current kernel (-background to specify value).
• -erosion — do a single erosion.
• -dilation — do a single dilation.
• -median_dilation — do a single median dilation. and bestie, read this twice: note: this is not a median filter! 🚨
• -open — open: dilation(erosion(X))
• -close — close: erosion(dilation(X))
• -lowpass — lowpass filter: close(open(X))
• -highpass — highpass filter: X - lowpass(X)
• -convolve — convolve file with kernel.
• -distance — distance transform.
• -group — label groups in ascending order.

⭐ Successive morphological operations ⭐

• -successive — successive operations (maximum: 100). you stack up a whole little alphabet of moves and she runs them in order. here's the alphabet, iykyk:

B[floor:ceil:fg:bg] - binarise in the range, using foreground and background
K[floor:ceil:bg] - clamp between the specified range. Set other voxels to 'bg' (default: 0)
P[bg] - pad volume with respect to the current kernel using 'bg' (default: 0)
E - erosion
D - dilation
M - median dilation
O - open
C - close
L - lowpass filter
H - highpass filter
X - convolve
F - distance transform (binary input only - not checked)
G - Label the groups in the volume in ascending order
R[TYPE|file.kern] - (2D04|2D08|3D06|3D26) or read in a kernel file
W[file.mnc] - write out current results
I[cmp.mnc] - local xcorr between current file and cmp.mnc

Default: "B" — she starts with B and that's just the way it is. 💅

fr fr though, that F line says binary input only - not checked, which means nobody's gonna stop you if you feed it something else. no vibe check, no safety net. be careful out there. 🫠

👑 Generic options for all commands 👑

• -help — print summary of command-line options and abort.
• -version — print version number of program and exit.

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🍓 EXAMPLE 🍓

mincmorph -help

look at her go. iconic behaviour, honestly. ✨

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and that's the whole page, bestie — go forth and morph some volumes, you've got this 💜🦋🌸✨🎀💖

this masterpiece was brought to you by mincmorph 2.3.00, dated July 2020. slay forever. 👑💅✨