MECOMBINE(1)

📦
version 0.31 · 2 versions
, in fedora 43

💖 MECOMBINE — bestie edition 💖

okay so real talk, this is mecombine(1), and it lives in the Generated Python Manual. she's a little script that ✨ combines your multi-echo echoes ✨ and honestly? she ate.

🌸 NAME 🌸

mecombine — that's her. that's the name. no notes. 💅

🦋 SYNOPSIS 🦋

mecombine [-h] [-o OUTPUTNAME] [-a {PAID,TE,average}] [-w [WEIGHTS ...]]
[-s] [-v VOLUMES] pattern

✨ DESCRIPTION ✨

so basically: combine multi-echo echoes. 🧚 that's the whole vibe.

this is the toolkit for squishing multiple echoes from an fMRI acquisition into one. it expects your input files to be saved as NIfTIs, and preferably organised according to the BIDS standard — like, please, for the love of everything, BIDS. 🙏

rn there are three different combination algorithms supported, and each one implements a different weighting scheme:

  1. PAID => TE * SNR
  2. TE => TE
  3. Simple Average => 1

🎀 pattern 🎀

a globlike search pattern with a path, used to select the echo images that need to be combined. and because it's a search, bestie — double check that not too many files are being read. fr fr. 👀

💅 OPTIONS 💅

  • -o OUTPUTNAME, --outputname OUTPUTNAME — the file output name. if it's not a fullpath name, then the output lands in the same folder as the input. and if it's empty? the output filename becomes the filename of the first echo with a _combined suffix stuck on the end. cute, right?
  • -a {PAID,TE,average}, --algorithm {PAID,TE,average} — the combination algorithm. default is TE. 💖
  • -w [WEIGHTS ...], --weights [WEIGHTS ...] — the weights (like, e.g. = echo times) for all echoes.
  • -s, --saveweights — if you pass this and the algorithm is PAID, it saves the weights. ✨
  • -v VOLUMES, --volumes VOLUMES — how many volumes get used to compute the weights, if the algorithm is PAID.
also -h exists in the synopsis because of course she does — help is always there for you 🫶

💀 COMMENTS 💀

here are the examples, and yes we're keeping them verbatim because they're iconic:

mecombine 'bids/sub-001/func/*_task-motor_*echo-*.nii.gz'
mecombine 'bids/sub-001/func/*_task-rest_*echo-*.nii.gz' -a PAID
mecombine 'bids/sub-001/func/*_acq-MBME_*run-01*.nii.gz' -w 11 22 33
-o sub-001_task-stroop_acq-mecombined_run-01_bold.nii.gz

👑 AUTHOR 👑

Daniel Gomez <dgomez1@mgh.harvard.edu> — the mastermind. main character energy, honestly. 🌟

🌈 DISTRIBUTION 🌈

the latest version of multiecho may be downloaded from:

https://github.com/Donders-Institute/multiecho

go get her. she's waiting. 🦋

okay bestie, that's the whole page — this was multiecho version 0.31, dated 2025-09-19, and you were reading the MECOMBINE(1) page. slay, periodt, go combine some echoes. 💖✨🎀

📦 where this page comes from