[J7F9] Pipeline reproduction (SPM - deriv)

[bclenet]

Softwares

SPM12, Update 7219
fmriprep, version 1.1.4
Matlab R2017b

Input data

derivatives (fMRIprep)

Additional context

• Hypotheses 1, 3, 6 and 8 provide unsufficient correlations with the original team results (see values below in the comments).

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]

PR #80 merged to main : J7F9 refactored.

The code allows to get the following correlation results (hypothesis 1 to 9).
0.9131411735231
0.957296569265423
0.9131411735231
0.957296569265423
0.9843141125089053
0.9058252041092889
0.9843141125089053
0.9058252041092889
0.952892940943768

Note

Subjects 005 and 043 produce errors during the subject level analysis (find crash files attached), hence the previous results are computed with 106 subjects.

crash-20240105-132640-root-model_design.a1-633d06b2-d0c4-4794-9c44-6a6c934f184c.txt
crash-20240105-132603-root-model_design.a0-ed511adc-d88f-4eb5-bd26-6e9d0e236546.txt

[cmaumet]

Given that all correlations are above 0.90, I think that we can consider this as a successful reproduction and therefore close this PR. @bclenet let me know if I missed something!

[bclenet]

@cmaumet there are unexplained crashes with sub-005 and sub-043 (see comment above), we will keep a track of this bug in the issue.
But sure, we can mark this pipeline as done :)