[T54A] Pipeline reproduction (FSL - deriv)

[bclenet]

Softwares

FSL v 5.0.9; RRID:SCR_002823 , fmriprep v.1.1.4

Input data

derivatives (fMRIprep)

Additional context

This pipeline is (almost) reproduced, only refactoring should be needed.

List of tasks

Please tick the boxes below once the corresponding task is finished. :+1:

• [x] :ok_hand: A maintainer of the project approved the issue, by assigning a :checkered_flag:status: ready for dev label to it.
• [x] :deciduous_tree: Create a branch on your fork to start the reproduction.
• [x] :sunrise: Create a file team_{team_id}.py inside the narps_open/pipelines/ directory. You can use a file inside narps_open/pipelines/templates as a template if needed.
• [ ] :inbox_tray: Create a pull request as soon as you completed the previous task.
• [x] :brain: Write the code for the pipeline, using Nipype and the file architecture described in docs/pipelines.md.
• [x] :blue_book: Make sure your code is documented enough.
• [x] :snake: Make sure your code is explicit and conforms with PEP8.
• [x] :microscope: Create tests for your pipeline. You can use files in tests/pipelines/test_team_* as examples.
• [ ] :microscope: Make sure your code passes all the tests you created (see docs/testing.md).

[bclenet]

Here are the correlation results for T54A. Improvement is needed.

Team	Number of subjects	Test status	Correlation values
T54A	108	failure	[0.83, 0.72, 0.83, 0.72, 0.70, 0.70, 0.70, 0.70, -0.01]

[bclenet]

It looks like the regressors of interest are not orthogonalized in the code, although mentioned in the description (section independent_vars_first_level):

• Gain: Modeled for trials with a valid response (Not NoResp), [...], orthoganlized with respect to the constant factor.
• Loss: Modeled for trials with a valid response (Not NoResp), [...], orthoganalized with respect to the constant factor.
• Difficulty: Modeled for trials with a valid response (Not NoResp), [...], orthogonalized with respect to the constant factor.

This can be done using the orthogonalization parameter in FSL's Level1Design.