ECHOCOMBINE(1)

📦
version 4.6.2 · 2 versions
, in fedora 43

💖 ECHOCOMBINE(1) 💖

okay bestie, welcome to ECHOCOMBINE(1) — the manual page for echocombine, and honestly? it's giving "tiny tool, huge main character energy". let's get into it 🫶

✨ NAME ✨

echocombine — no cap, that's the whole name. short, sweet, iconic.

🌈 SYNOPSIS 🌈

echocombine [-h] [-p LABEL [LABEL ...]] [-o DESTINATION] [-a
       {PAID,TE,average}] [-w [WEIGHT ...]] [-f] bidsfolder pattern

💅 DESCRIPTION 💅

so what IS this? echocombine is a wrapper around the 'mecombine' multi-echo combination tool (the og lives at https://github.com/Donders-Institute/multiecho). it's basically the friendly bestie that holds your hand while you do the thing.

except for BIDS inheritances (iykyk), this wrapper is BIDS-aware — it's a 'bidsapp' — and it writes BIDS compliant output. slay. ✨

  • bidsfolder — the bids-directory with the (multi-echo) subject data. that's your home base, bestie 🏠
  • pattern — a globlike recursive search pattern (relative to the subject/session folder) that selects the first echo of the images that need to be combined. for example '*task-*echo-1*'. literally just tell it which echo-1 files to look for and it does the rest 💫

🎀 OPTIONS 🎀

  • -p LABEL [LABEL ...], --participant LABEL [LABEL ...] — a space separated list of sub-# identifiers to be processed (the sub- prefix can be left out, we're not gonna make you type it 💀). if you don't specify this, then all participants get processed. all of them. the whole squad 👑
  • -o DESTINATION, --output DESTINATION — a string that determines where the output is saved. it can be the name of a BIDS datatype folder, like 'func', or of the derivatives folder, i.e. 'derivatives'. and if output is left empty? then the combined image is saved in the input datatype folder, and the original echo images get moved to the 'extra_data' folder. so like, they're not gone, they're just chillin elsewhere 🦋
  • -a {PAID,TE,average}, --algorithm {PAID,TE,average} — the combination algorithm. pick your fighter: PAID, TE, or average ✨
  • -w [WEIGHT ...], --weights [WEIGHT ...] — weights for each echo. one for you, one for you, one for you 💅
  • -f, --force — process all images, regardless of whether target images already exist. otherwise (aka without this flag) the echo-combination will be skipped. so if you're wondering why nothing happened — yeah, that's why, bestie 😭

🧚 COMMENTS 🧚

examples, because seeing it in action is so much better than reading about it:

echocombine myproject/bids func/*task-stroop*echo-1*
echocombine myproject/bids *task-stroop*echo-1* -p 001 003
echocombine myproject/bids func/*task-*echo-1* -o func
echocombine myproject/bids func/*task-*echo-1* -o derivatives -w 13 26 39 52
echocombine myproject/bids func/*task-*echo-1* -a PAID

👑 AUTHOR 👑

Marcel Zwiers <m.zwiers@donders.ru.nl> — the legend themselves 🫶

and that's the whole page, bestie!! this was bidscoin version 4.6.2, dated 2025-11-06, and honestly? iconic. go combine some echoes, you got this 💖✨🎀

📦 where this page comes from