T2* mapping model

[jvelazquez-reyes]

Purpose

T2* mapping model working with default parameters

Open Questions and Pre-Merge TODOs

• Use github checklists. When solved, check the box and explain the answer.

• Review that changed source files/lines are related to the pull request/issue
  If any files/commits were accidentally included, cherry-pick them into another branch.

• Review that changed source files/lines were not accidentally deleted
  Fix appropriately if so.

• Test new features or bug fix
  If not implemented/resolved adequately, solve it or inform the developer by requesting changes in your review.
  Preferably, set breakpoints in the locations that the code was changed and follow allong line by line to see if the code behaves as intended.

Manual GUI tests (general)

• Does the qMRLab GUI open?
• Can you change models?
• Can you load a data folder for a model?
• Can you view data?
• Can you zoom in the image?
• Can you pan out of the image?
• Can you view the histogram of the data?
• Can you change the color map?
• Can you fit dataset (Fit data)?
• Can you save/load the results?
• Can you open the options panel?
• Can you change option parameters?
• Can you save/load option paramters?
• Can you select a voxel?
• Can you fit the data of that voxel ("View data fit")?
• Can you simulate and fit a voxel ("Single Voxel Curve")?
• Can you run a Sensitivity Analysis?
• Can you simulate a Multi Voxel Distribution?

[codecov]

Codecov Report

Merging #445 (f24407b) into usrjson (e2d2140) will decrease coverage by 1.09%.
The diff coverage is 47.04%.

@@             Coverage Diff             @@
##           usrjson     #445      +/-   ##
===========================================
- Coverage    47.40%   46.30%   -1.10%     
===========================================
  Files          260      282      +22     
  Lines         8647    10370    +1723     
===========================================
+ Hits          4099     4802     +703     
- Misses        4548     5568    +1020     

Flag	Coverage Δ
matlab	45.48% <46.55%> (-1.14%)	⬇️
octave	38.37% <46.26%> (+1.22%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/Common/AbstractModel.m	75.00% <ø> (+8.75%)	⬆️
src/Common/FitResultsSave_BIDS.m	0.00% <0.00%> (ø)
src/Common/qMRFit_BIDS.m	0.00% <0.00%> (ø)
src/Common/qMRLab_static_Models.m	0.00% <0.00%> (ø)
src/Common/units/validatePanelUnits.m	0.00% <0.00%> (ø)
...els_Functions/MP2RAGE/func/T1B1correctpackageTFL.m	84.74% <ø> (ø)
src/Models_Functions/T2star/TA_rget.m	0.00% <0.00%> (ø)
src/Models_Functions/T2star/conv3.m	0.00% <0.00%> (ø)
src/Models_Functions/T2star/stat_nlleasqr.m	0.00% <0.00%> (ø)
.../Models_Functions/T2star/t2star_computeGradientZ.m	0.00% <0.00%> (ø)
... and 46 more

---

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 e2d2140...f24407b. Read the comment docs.

[agahkarakuzu]

@jvelazquez-reyes for tests we may consider a really small dataset for this model.

[jvelazquez-reyes]

Is there any available on OSF?

[agahkarakuzu]

Not yet, but if you can crop the images to a smaller extent, we can add it.

[agahkarakuzu]

Great! Let's make sure that the test actually runs for this model. Then we'll merge usejson first to master.

[agahkarakuzu]

@jvelazquez-reyes see this error.

The test is failing because the filenames you provide for the example dataset do not match those in InputNames of the model.

Current file names:
magnitude.nii.gz phase.nii.gz

Required file names:
DATAmag.nii.gz DATAphase.nii.gz

That's how genBatch infers which file to load to which field.

Can you also update the mono_t2star header comment to make separate entries for them?

[jvelazquez-reyes]

I see, thanks!

What names would you prefer to keep? magnitude.nii.gz or DATAmag.nii.gz?

[agahkarakuzu]

It is not really up to my preference :) Please see the wiki docs:

https://github.com/qMRLab/qMRLab/wiki/Guideline:-Uploading-sample-data

[agahkarakuzu]

Cool, I like Magn and Phase better and now they match OSF vs Model 👍