add methods section

giga_connectome/data/methods/template.jinja

@@ -0,0 +1,25 @@
+These results were generated with giga_connectome (version {{ data.version }}, https://giga-connectome.readthedocs.io/en/latest/).
+
+The following steps were followed.
+
+1. Created subject specific grey matter mask in MNI space.
+
+2. Sampled the atlas to the space of subject specific grey matter mask in MNI space.
+
+3. Calculated the conjunction of the customised grey matter mask and resampled atlas to find valid parcels.
+
+4. Used the new input specific grey matter mask and atlas to extract time series and connectomes for each subject.
+   The time series data were denoised as follow:
+
+    - Time series extractions through label or map maskers are performed on the denoised nifti file.
+    - Denoising steps were performed on the voxel level:
+        - spatial smoothing
+        - detrend, only if high pass filter was not applied through confounds
+        - Regress out confounds
+        - standardize
+    - Extracted time series from atlas
+    - Computed correlation matrix
+
+5. Calculate intranetwork correlation of each parcel. The values replace the diagonal of the connectomes.
+
+6. Create a group average connectome.

giga_connectome/methods.py

@@ -0,0 +1,27 @@
+"""Module responsible for generating method section."""
+
+from pathlib import Path
+
+from jinja2 import Environment, FileSystemLoader, select_autoescape
+
+from giga_connectome import __version__
+
+
+def generate_method_section(output_dir: Path):
+
+    env = Environment(
+        loader=FileSystemLoader(Path(__file__).parent),
+        autoescape=select_autoescape(),
+        lstrip_blocks=True,
+        trim_blocks=True,
+    )
+
+    template = env.get_template("data/methods/template.jinja")
+
+    output_file = output_dir / "logs" / "CITATION.md"
+    output_file.parent.mkdir(parents=True, exist_ok=True)
+
+    data = {"version": __version__}
+
+    with open(output_file, "w") as f:
+        print(template.render(data=data), file=f)

giga_connectome/tests/test_methods.py

@@ -0,0 +1,5 @@
+from giga_connectome import methods
+
+
+def test_generate_method_section(tmp_path):
+    methods.generate_method_section(output_dir=tmp_path)

pyproject.toml

@@ -26,6 +26,7 @@ dependencies = [
   "templateflow < 23.0.0",
   "tqdm",
   "setuptools",
+  "jinja2 >= 2.0",
 ]
 dynamic = ["version"]