EHN edit docs to fit the new structure

Makefile

@@ -18,5 +18,5 @@ data:
 book:
 	jb build content --all
 
-figures: inputs/fmriprep-denoise-benchmark/denoise-metrics
+figures: data/fmriprep-denoise-benchmark/denoise-metrics
 	$(PYTHON) scripts/make_manuscript_figures.py

README.md

@@ -16,6 +16,7 @@ virtualenv env
 source env/bin/activate
 pip install -r binder/requirements.txt
 pip install .
+make data
 make book
 ```
 
@@ -25,7 +26,7 @@ make book
 
 - `content/` is the source of the JupyterBook.
 
-- `inputs/` is reserved to store data for building the JupyterBook.
+- `data/` is reserved to store data for building the JupyterBook.
   To build the book, one will need all the metrics from the study.
   The metrics are here:
   [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7764979.svg)](https://doi.org/10.5281/zenodo.7764979)

content/docs/setup.md

@@ -24,10 +24,12 @@ After cloning and setting up the project, we will need to get all the atlases fo
 
 ### Option 1: Download the atlas
 
-You can download a customised tempalteflow directory, untar into `inputs/`.
+You can download the customised tempalteflow directory, untar into `data/`.
+For the purpose of separating processing and book building, we will copy the templates to `inputs/custome_templateflow`
 
 ```bash
-make atlas
+make data
+cp -r data/fmriprep-denoise-benchmark/custome_templateflow inputs/custome_templateflow
 ```
 
 ### Option 2: Generate the atlas

content/docs/tldr.md

@@ -14,10 +14,12 @@ or help me edit the manuscript, the instruction is as followed:
 ```{code-block} bash
 git clone --recurse-submodules https://github.com/SIMEXP/fmriprep-denoise-benchmark.git
 cd fmriprep-denoise-benchmark
-virtualenv env 
-sourse env/bin/activate
+virtualenv env
+source env/bin/activate
 pip install -r binder/requirements.txt
-make all
+pip install .
+make data
+make book
 ```
 :::
 

fmriprep_denoise/features/derivatives.py

@@ -9,7 +9,7 @@
 
 MOTION_QC_FILE = "motion_qc.json"
 project_root = Path(__file__).parents[2]
-inputs = project_root / "inputs"
+inputs = project_root / "data"
 group_info_column = {"ds000228": "Child_Adult", "ds000030": "diagnosis"}
 
 

fmriprep_denoise/visualization/utils.py

@@ -48,7 +48,7 @@ def repo2data_path():
 def get_data_root():
     """Get motion metric data path root."""
     default_path = Path(__file__).parents[2] / \
-        "inputs" / "fmriprep-denoise-benchmark"
+        "data" / "fmriprep-denoise-benchmark"
     if not (default_path / "data_requirement.json").exists():
         default_path = repo2data_path()
     return default_path

scripts/fetch_templates.py

@@ -44,7 +44,7 @@ def download_difumo():
 
 
 def main():
-    tf_dir = Path(__file__).parents[1] / "inputs" / \
+    tf_dir = Path(__file__).parents[1] / "data" / \
         "fmriprep-denoise-benchmark" / "custome_templateflow"
     os.environ["TEMPLATEFLOW_HOME"] = str(tf_dir.resolve())
 

scripts/setup_templateflow.sh

@@ -1,6 +1,6 @@
 # set up the project after cloneing
 # Move templates to locations you need them to be
-# This is saved for record keeping. To download the files please use command `make atlas``
+# This is saved for record keeping. To download the files please use command `make data``
 #!/bin/bash
 
 # mist