[80GC] Pipeline reproduction (AFNI - deriv)

[JLefortBesnard]

Softwares

AFNI

Input data

derivatives (fMRIprep)

Additional context

This pipeline is used without Nipype, so far.

List of tasks

Please tick the boxes below once the corresponding task is finished. 👍

• 👌 A maintainer of the project approved the issue, by assigning a 🏁status: ready for dev label to it.
• 🌳 Create a branch on your fork to start the reproduction.
• 🌅 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.
• 📥 Create a pull request as soon as you completed the previous task.
• 🧠 Write the code for the pipeline, using Nipype and the file architecture described in docs/pipelines.md.
• 📘 Make sure your code is documented enough.
• 🐍 Make sure your code is explicit and conforms with PEP8.
• 🔬 Create tests for your pipeline. You can use files in tests/pipelines/test_team_* as examples.
• 🔬 Make sure your code passes all the tests you created (see docs/testing.md).

[bclenet]

Correlation results with 108 subjects : [0.69, 0.75, 0.69, 0.75, 0.69, 0.74, 0.69, 0.74, -0.29] (commit bc9d7c7)

One issue could be the mask creation for 3dttest++. Currently we create mask intersection for N subjects (one half from the equalRange group, one half from the equalIndifference), and use this mask to compute the 1 sample t-test on both groups (i.e.: N/2 subject in both case). This is done because 3dttest++ allows to compute 1 sample t-test as well as 2 sample t-test (for group comparison) in the same call.

Note that the thresholded maps are not computed with this version of the code. This could be done by creating an interface for 3dClustSim.