[FIX] Remove hardcoded numbers of echoes.

[tsalo]

Closes #77.

Changes proposed in this pull request:

• Remove hardcoded number of echoes from Kappa/Rho calculations.
• Remove hardcoded number of echoes from adaptive mask creation.

[codecov]

Codecov Report

Merging #95 into master will not change coverage.
The diff coverage is 60%.

@@           Coverage Diff           @@
##           master      #95   +/-   ##
=======================================
  Coverage   42.74%   42.74%           
=======================================
  Files          27       27           
  Lines        1516     1516           
=======================================
  Hits          648      648           
  Misses        868      868

Impacted Files	Coverage Δ
tedana/model/fit.py	8.08% <0%> (ø)	⬆️
tedana/utils/utils.py	83.85% <100%> (ø)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update bfaec06...92201f2. Read the comment docs.

[handwerkerd]

I don't think the removal of '/ 3' in utils.py is a number of echoes issue.

tedana/tedana/utils/utils.py

Line 200 in bfaec06

lthrs = np.squeeze(echo_means[med_val].T) / 3 # QUESTION: why divide by 3?

Looking at the code above and below, this function is a simple, but arbitrary way to create a voxelwise mask. It makes the assumption that at least 1/3 of the volume isn't in the brain and it finds the voxel with the 33rd percentile magnitude in the first echo. It then uses the same voxel for all 3 echoes since it's assumed to be an out-of-brain voxel. It takes a threshold from each echo and uses that to define the echo-specific masking threshold. The '/ 3' seems to be used to set the threshold to 1/3 of the selected voxel in each echo so that you only exclude voxels that are really noise. Both the 33rd percentile and the divide by 3 steps seem like arbitrary thresholds, but the division by 3 doesn't look like it has anything to do with the number of echoes so it shouldn't be changed.

Also, this is passing CI, but does any of the sample data this is being tested on include more than 3 echoes? If not, then this change wouldn't alter the output.

[tsalo]

That makes sense. I'll change that function back.

[emdupre]

WDYT of flagging that value as arbitrary in the code comments, @tsalo ? Maybe with a # NOTE: ?

[tsalo]

@emdupre That's a great idea! Adding notes now.

[emdupre]

LGTM ! I'm ok to merge this in and then re-visit when we add additional tests from other 4+ echo datasets. WDYT @handwerkerd, @tsalo ?