FIX: Order of SPM.NewSegment channel_info boolean tuple is (Field, Corrected)

[servoz]

Summary

• In SPM12, for Segment module (the NewSegment in Nipype), the spm.spatial.preproc.channel.write parameter (SPM's Save Bias Corrected parameter) takes [Save Bias Field = 0 or 1, Save Bias Corrected = 0 or 1]. In nypipe the initialisation of the outputs bias_field_images and bias_corrected_images are done with the inverse order.

List of changes proposed in this PR (pull-request)

• This commit fix this inconsistency.

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[codecov-io]

Codecov Report

Merging #2817 into master will increase coverage by 0.05%.
The diff coverage is 0%.

@@            Coverage Diff             @@
##           master    #2817      +/-   ##
==========================================
+ Coverage   67.48%   67.53%   +0.05%     
==========================================
  Files         341      341              
  Lines       43343    43462     +119     
  Branches     5375     5401      +26     
==========================================
+ Hits        29248    29352     +104     
- Misses      13396    13408      +12     
- Partials      699      702       +3

Flag	Coverage Δ
#smoketests	50.55% <0%> (ø)	⬆️
#unittests	64.95% <0%> (+0.04%)	⬆️

Impacted Files	Coverage Δ
nipype/interfaces/spm/preprocess.py	57.03% <0%> (ø)	⬆️
nipype/testing/utils.py	91.37% <0%> (+1.72%)	⬆️
nipype/interfaces/fsl/epi.py	69.14% <0%> (+4.94%)	⬆️

---

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 35b58cd...d5137c3. Read the comment docs.

[effigies]

If I'm understanding you correctly, users were submitting valid (bool, bool) pairs that were being correctly interpreted by SPM, but Nipype was misinterpreting them, and specifying the wrong output?

It looks like this was written for SPM8 and adapted to support SPM12. Is it possible that the order switched in SPM12? If so, the correct response might be to reverse that tuple if SPM12 is detected, and make a note of it in the docstring.

[servoz]

@effigies ,
i just checked:
In SPM8:
New Segment module:
spm.tools.preproc8.channel.write = [0 1] # Save Bias Corrected (only)
spm.tools.preproc8.channel.write = [1 0] # Save Bias Field (only)

As fas as I can check, in SPM8 the first element of the write list is concerning to the Bias Field (BiasField_aName.nii) and the second the Bias Corrected image (maName.nii) ... It is exactly the same in SPM12 (my first post). You invert in nipype! We currently overload the corresponding nipype class in our project. It will be cleaner if you fix it by merging my PR !

[effigies]

Okay, this seems like a good fix to me.

@chrisfilo, looks like you originally wrote this interface, so I want to give you veto, in case you remember some reason this was the way it was.

[chrisgorgo]

I don't see anything wrong here, but I have not used SPM in ages.