[pipeline in progress] Create a pipeline for GE2REC project

[manuegrx]

As part of the GE2REC project, we would like to create a new pipeline in open access for mapping the language-and-memory network (LMN) using 3 fMRI sequences acquired in the GE2REC protocol (more info here.

The pipeline will reproduce SPM batch and was partially already in AMIGO. The development are in this branch : https://github.com/populse/mia_processes/tree/ge2rec
A first version of the pipeline is already working but there are still improvements and checks to be made and the report needs to be linked to the pipeline and improved.

To do (non-exhautive, will be updated) : pipeline :

1. Change preprocessing part to add Slice timing correction
2. Add behavioral data
3. Add analysis with behavioral data
4. Compare result from SPM

report:

1. Add lateralization index: usually done with Li toolbox, but Matlab or SPMStabdalone with the toolboxe needed so the aim is to explore what is possible without this toolboxe
2. Add behavioral data
3. Add figure for analysis with behavioral data
4. See how to choose the color bar for spmT
5. Report in CVR report the use of a function to get realignment figure
6. See if it is possible / useful to add an automatic conclusion
7. Validate the report

[manuegrx]

The main development of this pipeline have been completed. Two pipelines have been added in the main branch : one with the behavioral data (with E-Prime file) and one without (see merge : https://github.com/populse/mia_processes/commit/a9697d86dd8e6eb2abfc3631fb255b4699e99011 )

I'm not closing this ticket yet because there's still work to be done :

• validate the pipeline with the latest version of the E-Prime file (waiting for a pilot subject)
• check all the subject information in the report (waiting for a pilot subject)
• validate the report with the final users (waiting for a pilot subject + meeting with users)
• add others masks for lateralization (waiting for the data)