update FAQ to help structure data to run stats on fmriprep

docs/source/FAQ.md

@@ -333,6 +333,90 @@ See those
 for some pointers on how to make choices for the resolution to choose for your
 analysis.
 
+## Statistics
+
+### How should I structure my data to run my statistical analysis?
+
+The main thing to remember is that CPP SPM will read the events.tsv files from
+your raw BIDS data set and will read the bold images from a `cpp_spm-preproc`
+folder.
+
+If your data was preprocessed with fmriprep, cpp_spm will first need to copy,
+unzip and smooth the data into a `cpp_spm-preproc` folder
+
+Here is an example of how the data is organized for the MoAE fmriprep demo and
+what the `cpp_spm` bids call would look like.
+
+```bash
+├── inputs
+│   ├── fmriprep                     # fmriprep preprocessed BIDS dataset
+│   |   ├── dataset_description.json
+│   │   └── sub-01
+│   │       ├── anat
+│   │       ├── figures
+│   │       └── func
+│   │           ├── sub-01_task-auditory_desc-confounds_timeseries.json
+│   │           ├── sub-01_task-auditory_desc-confounds_timeseries.tsv
+│   │           ├── sub-01_task-auditory_space-MNI152NLin6Asym_desc-brain_mask.json
+│   │           ├── sub-01_task-auditory_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
+│   │           ├── sub-01_task-auditory_space-MNI152NLin6Asym_desc-preproc_bold.json
+│   │           └── sub-01_task-auditory_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
+│   └── raw                          # raw BIDS dataset
+│       ├── dataset_description.json
+│       ├── README
+│       ├── sub-01
+│       │   ├── anat
+│       │   │   └── sub-01_T1w.nii
+│       │   └── func
+│       │       ├── sub-01_task-auditory_bold.nii
+│       │       └── sub-01_task-auditory_events.tsv
+│       └── task-auditory_bold.json
+├── models                            # models used to run the GLM
+│   ├── model-MoAEfmriprep_smdl.json
+│   ├── model-MoAEindividual_smdl.json
+│   └── model-MoAE_smdl.json
+├── options
+└── outputs
+    └── derivatives
+        └── cpp_spm-preproc          # contains either data taken from fmriprep and smoothed
+            ├── dataset_description.json
+            ├── README
+            ├── jobs
+            │   └── auditory
+            │       └── sub-01
+            └── sub-01
+                ├── anat
+                └── func
+                    ├── sub-01_task-auditory_desc-confounds_timeseries.json
+                    ├── sub-01_task-auditory_desc-confounds_timeseries.tsv
+                    ├── sub-01_task-auditory_space-MNI152NLin6Asym_desc-brain_mask.json
+                    ├── sub-01_task-auditory_space-MNI152NLin6Asym_desc-brain_mask.nii
+                    ├── sub-01_task-auditory_space-MNI152NLin6Asym_desc-preproc_bold.json
+                    ├── sub-01_task-auditory_space-MNI152NLin6Asym_desc-preproc_bold.nii
+                    ├── sub-01_task-auditory_space-MNI152NLin6Asym_desc-smth8_bold.json
+                    └── sub-01_task-auditory_space-MNI152NLin6Asym_desc-smth8_bold.nii
+```
+
+```matlab
+WD = fileparts(mfilename('fullpath'));
+
+subject_label = '01';
+
+bids_dir = fullfile(WD, 'inputs', 'raw');
+output_dir = fullfile(WD, 'outputs', 'derivatives');
+preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
+
+model_file = fullfile(pwd, 'models', 'model-MoAEfmriprep_smdl.json');
+
+cpp_spm(bids_dir, output_dir, 'subject', ...
+        'participant_label', {subject_label}, ...
+        'action', 'stats', ...
+        'preproc_dir', preproc_dir, ...
+        'model_file', model_file, ...
+        'fwhm', 8, ...
+        'options', opt);
+```
+
 ## Results
 
 ### How can I change which slices are shown in a montage?