christinadelta / FSLpipeline_masters

The pipeline that I used to analyse my fMRI data for my master's project

FSL pipeline for my masters project

The pipeline that I used to analyse my fMRI data for my master's project

This has not been used ever since then (2017)!

Dependencies: FSL, python3 and FreeSurfer (in some cases)

The steps of the pipeline to run an fMRI analysis using python scripts and FSL:

• Step 1: check all your anatomical and bolds paths etc and run bet (bet extraction)
• Step 2: prepare the functional data
• Step 3: make FSF for level 1 analysis
• check your level 1 outputs
• Step 4: make fsf FOR level 2 analysis (within)
• check your level 2 outputs
• Step 5: runs level 3 (group level) analysis
• check your level 3 outputs

NOTE:

These scripts run in combination with GUI interaction (FEAT). For example, I prefer to do a lot of pre-processing stuff (like motion correction, etc.., through FEAT). Also, analysis of level 3 (step 5 is done through FEAT entirely).