demo for using mean functional image mask

[CerenB]

It contains a function bidswholeBrainFuncMask which is using cpp-spm segmentation and skullstripping scripts on the mean functional image. The end product is binary mask for the segmented-skullstripped-mean functional image.

• can be used to mask analysis (to get rid off smoothing spillover effects)
• can be used when GLM will not be performed but still whole brain functional mask is need for some analysis (e.g. FFT)

[codecov]

Codecov Report

Merging #353 (531ac49) into dev (bebca72) will decrease coverage by 0.09%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev     #353      +/-   ##
==========================================
- Coverage   60.58%   60.49%   -0.10%     
==========================================
  Files         115      115              
  Lines        1865     1868       +3     
==========================================
  Hits         1130     1130              
- Misses        735      738       +3     

Impacted Files	Coverage Δ
src/getPrefix.m	100.00% <ø> (ø)
src/workflows/bidsWholeBrainFuncMask.m	0.00% <ø> (ø)
src/workflows/bidsResults.m	0.00% <0.00%> (ø)

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[Remi-Gau]

Don't worry too much if you still get some errors with miss hit: we can clean those up a bit later on the dev branch itself or in another PR. :-)

[CerenB]

perseverance... the mh fix should be done now! let me know what you think!

[CerenB]

So this PR has been ready to be merged.
Though, when I use below function in MNI space (not in individual), there are some holes in mostly basal ganglia in the masks.
mask = bidsWholeBrainFuncMask(opt);
I'm using also different ImcalcDefault option (16bits).

Any ideas why it would happen? Not that I need to resolve this issue asap, mostly I'm wondering...

[Remi-Gau]

OK @CerenB don't panic about the large number of new files committed as pre-commit weny a bit crazy and let miss_hit clean all our libraries...

[Remi-Gau]

So this PR has been ready to be merged.
Though, when I use below function in MNI space (not in individual), there are some holes in mostly basal ganglia in the masks.
mask = bidsWholeBrainFuncMask(opt);
I'm using also different ImcalcDefault option (16bits).

Any ideas why it would happen? Not that I need to resolve this issue asap, mostly I'm wondering...

I checked and lowering the skull stripping threshold eventually worked at including all the stuff in the basal ganglia

opt.skullstrip.threshold = 0.5;