[FIX] remove extra submodules and properly compute run level contrasts

[Remi-Gau]

fixes #415
fixes #416

[Remi-Gau]

This should also fix the fact that all tests were failing on main.

Required to update the bids-matlad and cpp_roi submodule and to a lot of tinckering.

[codecov]

Codecov Report

Merging #418 (816f73d) into main (d77c17d) will increase coverage by 0.90%.
The diff coverage is 78.75%.

@@            Coverage Diff             @@
##             main     #418      +/-   ##
==========================================
+ Coverage   59.69%   60.60%   +0.90%     
==========================================
  Files         120      120              
  Lines        1965     2000      +35     
==========================================
+ Hits         1173     1212      +39     
+ Misses        792      788       -4     

Impacted Files	Coverage Δ
src/batches/setBatchEstimateModel.m	0.00% <0.00%> (ø)
src/batches/setBatchSubjectLevelGLMSpec.m	97.72% <ø> (ø)
src/batches/setBatchSubjectLevelResults.m	100.00% <ø> (ø)
src/defaults/createDefaultModel.m	96.87% <ø> (ø)
src/fieldmaps/getMetadataFromIntendedForFunc.m	0.00% <ø> (ø)
src/reports/copyFigures.m	0.00% <ø> (ø)
src/reports/reportBIDS.m	0.00% <0.00%> (ø)
src/workflows/bidsConcatBetaTmaps.m	0.00% <0.00%> (ø)
src/workflows/bidsCreateROI.m	0.00% <0.00%> (ø)
src/workflows/bidsCreateVDM.m	0.00% <0.00%> (ø)
... and 16 more

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[Remi-Gau]

@CerenB

The tests seem to pass so you can go ahead and test that branch.

Mind you that you will have to update the bids-matlab and cpp_roi submodule if git kraken does not do it for you.

[CerenB]

it works in gitkraken without any issues! I reviewed the changes for run level as well. now I'll run it on my local.
thank you for tagging me, reviewing helps, especially to learn "where to look for" to understand how the code works.

[CerenB]

@Remi-Gau I see there's a variable change from "type" to "suffix". I got error for that. it cannot find "suffix". I cannot find it either, can you give me some pointers?
I was running FFX

bidsFFX('specifyAndEstimate', opt, FWHM);

WORKFLOW: SUBJECT LEVEL GLM

Starting parallel pool (parpool) using the 'local' profile ...
connected to 4 workers.
 PROCESSING SUBJECT No.: 1 SUBJECT ID : 001 

 BUILDING JOB: specify subject level fmri model
/Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/s2wuasub-001_ses-001_task-PitchFT_run-001_bold.nii
reading the tsv file : /Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/sub-001_ses-001_task-PitchFT_run-001_events.tsv 
/Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/s2wuasub-001_ses-001_task-PitchFT_run-002_bold.nii
reading the tsv file : /Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/sub-001_ses-001_task-PitchFT_run-002_events.tsv 
/Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/s2wuasub-001_ses-001_task-PitchFT_run-003_bold.nii
reading the tsv file : /Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/sub-001_ses-001_task-PitchFT_run-003_events.tsv 
/Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/s2wuasub-001_ses-001_task-PitchFT_run-004_bold.nii
reading the tsv file : /Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/sub-001_ses-001_task-PitchFT_run-004_events.tsv 
/Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/s2wuasub-001_ses-001_task-PitchFT_run-005_bold.nii
reading the tsv file : /Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/sub-001_ses-001_task-PitchFT_run-005_events.tsv 
/Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/s2wuasub-001_ses-001_task-PitchFT_run-006_bold.nii
reading the tsv file : /Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/sub-001_ses-001_task-PitchFT_run-006_events.tsv 
/Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/s2wuasub-001_ses-001_task-PitchFT_run-007_bold.nii
reading the tsv file : /Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/sub-001_ses-001_task-PitchFT_run-007_events.tsv 
/Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/s2wuasub-001_ses-001_task-PitchFT_run-008_bold.nii
reading the tsv file : /Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/sub-001_ses-001_task-PitchFT_run-008_events.tsv 
/Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/s2wuasub-001_ses-001_task-PitchFT_run-009_bold.nii
reading the tsv file : /Users/battal/Cerens_files/fMRI/Processed/RhythmCateg/PitchFT/derivatives/cpp_spm/sub-001/ses-001/func/sub-001_ses-001_task-PitchFT_run-009_events.tsv 
Error using bids.create_filename (line 57)
We need at least a suffix to create a
filename.

Error in bidsFFX (line 71)
                                                                bids.create_filename(p))); 

[CerenB]

ok a bit further check also showed thatbids.reportfunction also fails on my local.
When I went back in my branch to v.1.1.0 it works there. in the bug-fix branch, I get this error:

bids.report(opt.dataDir)
Error using ismember>ismemberR2012a (line 178)
Input A of class char and input B of class logical must be the
same class, unless one is double.

Error in ismember (line 87)
        lia = ismemberR2012a(A,B);

Error in bids.query>perform_query (line 226)
    if ~ismember(this_subject.name(5:end), subjects)

Error in bids.query (line 101)
  result = perform_query(BIDS, query, options, subjects,
  modalities, target);

Error in bids.report>select_session (line 297)
  sessions = bids.query(BIDS, 'sessions', 'sub', sub);

Error in bids.report (line 68)
  [ses, nb_ses] = select_session(BIDS, p, sub);

[Remi-Gau]

I see there's a variable change from "type" to "suffix". I got error for that. it cannot find "suffix". I cannot find it either, can you give me some pointers?

arf... I must have overlooked some additional things to fix.

In brief, when updating the bids-matlab version in use, it means that we now have to update some of the code.

The old version of bids matlab would use the term 'type' to refer to what in the BIDS world is a 'suffix' (the _bold at the end of your func file for example).

Am suprised that the system test did not crash because of that, but once again that highlights the need to have full code coverage in the test suite... #BrokenRecord

Updating things now. Will run the full demos to make sure things are OK.

[Remi-Gau]

ok a bit further check also showed thatbids.reportfunction also fails on my local.
When I went back in my branch to v.1.1.0 it works there. in the bug-fix branch, I get this error:

That too is a bids-matlab issue: the report function is now broken and I must fix it.

So temporarily comment it out.

Will add a warning in our function in case people try to run it.

[Remi-Gau]

@CerenB Things should be fixed now.

[CerenB]

Wooop! calculating contrasts works on run level!

[Remi-Gau]

Awesome !!

Let's merge this baby