[DOC] add links in doc (#1269)

* add link to openneuro and fix some sphinx warnings * add links to SPM doc
cpp-lln-lab · Jul 8, 2024 · 41d5480 · 41d5480
1 parent 855a567
commit 41d5480
Show file tree

Hide file tree

Showing 11 changed files with 45 additions and 21 deletions.
diff --git a/demos/MoAE/README.md b/demos/MoAE/README.md
@@ -1,6 +1,6 @@
 # Mother of All Experiments
 
-This "Mother of All Experiments" is based on the block design of SPM.
+This ["Mother of All Experiments" is based on the block design of SPM](https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/fmri/block/).
 
 In the `options` folder has several examples of how to encode the options of
 your analysis in a json file.

diff --git a/demos/bayes/Makefile b/demos/bayes/Makefile
@@ -1,4 +1,4 @@
-.PHONY: clean data data_ds000001
+.PHONY: clean
 
 clean:
 	rm -rf inputs

diff --git a/demos/bayes/ds000114_run.m → demos/bayes/ds000114_bayes_run.m b/demos/bayes/ds000114_run.m → demos/bayes/ds000114_bayes_run.m
diff --git a/demos/face_repetition/README.md b/demos/face_repetition/README.md
@@ -1,5 +1,8 @@
 # Face repetition demo
 
+This is based on the [event related design dataset of SPM](https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/fmri/event/).
+
+
 ## CLI commands
 
 ### Preprocessing

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -79,9 +79,18 @@
 
 source_suffix = [".rst", ".md"]
 
-# intersphinx_mapping = {
-#     "bids-matlab": ("https://bids-matlab.readthedocs.io/en/main", None)
-# }
+intersphinx_mapping = {
+    "bids-matlab": ("https://bids-matlab.readthedocs.io/en/main", None),
+    "nilearn": ("https://nilearn.github.io/stable", None),
+}
+
+# We recommend adding the following config value.
+# Sphinx defaults to automatically resolve *unresolved* labels using all your Intersphinx mappings.
+# This behavior has unintended side-effects, namely that documentations local references can
+# suddenly resolve to an external location.
+# See also:
+# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_disabled_reftypes
+# intersphinx_disabled_reftypes = ["*"]
 
 coverage_show_missing_items = True
 

diff --git a/docs/source/demos/bayesian_model_selection.rst b/docs/source/demos/bayesian_model_selection.rst
@@ -5,14 +5,14 @@ Bayesian model selection
 
 .. automodule:: demos.bayes
 
-.. autoscript:: ds000114_run
+.. autoscript:: ds000114_bayes_run
 
 .. admonition:: script
     :class: dropdown
 
-    .. literalinclude:: ../../../demos/bayes/ds000114_run.m
+    .. literalinclude:: ../../../demos/bayes/ds000114_bayes_run.m
         :language: matlab
-        :caption: demos/bayes/ds000114_run.m
+        :caption: demos/bayes/ds000114_bayes_run.m
         :lines: 16-
 
 .. admonition:: Default BIDS stats model

diff --git a/docs/source/demos/face_repetition.rst b/docs/source/demos/face_repetition.rst
@@ -3,7 +3,7 @@
 Face repetition
 ***************
 
-This is based on the event related design dataset of SPM.
+This is based on the `event related design dataset of SPM <https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/fmri/event/>`_.
 
 .. automodule:: demos.face_repetition
 

diff --git a/docs/source/demos/moae.rst b/docs/source/demos/moae.rst
@@ -9,7 +9,8 @@ MoAE
         ├── models
         └── options
 
-This "Mother of All Experiments" is based on the block design dataset of SPM.
+This "Mother of All Experiments" is based on
+`the block design dataset of SPM <https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/fmri/block/>`_.
 
 In the ``options`` folder has several examples of how to encode the options of your
 analysis in a json file.

diff --git a/docs/source/demos/openneuro.md b/docs/source/demos/openneuro.md
@@ -9,6 +9,8 @@
 
 ## ds000001: Balloon analog risk
 
+- [Source dataset](https://openneuro.org/datasets/ds000001)
+
 ### Features
 
 -   one task
@@ -26,6 +28,8 @@
 
 ## ds000114: test-retest
 
+- [Source dataset](https://openneuro.org/datasets/ds000114)
+
 ### Features
 
 -   several tasks
@@ -40,6 +44,8 @@
 
 ## ds000224
 
+- [Source dataset](https://openneuro.org/datasets/ds000224)
+
 ### Scripts
 
 ```{eval-rst}
@@ -48,6 +54,8 @@
 
 ## ds001168
 
+- [Source dataset](https://openneuro.org/datasets/ds001168)
+
 ### Features
 
 -   resting state
@@ -62,16 +70,10 @@
 .. autoscript:: ds001168_run
 ```
 
-## ds002799: NARPS
-
-### Features
-
--   resting state and task
--   several sessions
--   fmriprep data
-
 ## ds001734: NARPS
 
+- [Source dataset](https://openneuro.org/datasets/ds001734)
+
 ### Features
 
 - one task
@@ -127,3 +129,13 @@ transformers cannot yet be appled to confounds
 ```{eval-rst}
 .. autoscript:: ds001734_run
 ```
+
+## ds002799
+
+- [Source dataset](https://openneuro.org/datasets/ds002799)
+
+### Features
+
+-   resting state and task
+-   several sessions
+-   fmriprep data
diff --git a/src/batches/setBatchSelectAnat.m b/src/batches/setBatchSelectAnat.m
@@ -10,7 +10,7 @@
   % :type  matlabbatch: structure
   %
   % :param BIDS: dataset layout.
-  %              See: bids.layout, getData.
+  %              See: :mat:func:`+bids.layout`, :func:`getData`.
   %
   % :type  BIDS: structure
   %

diff --git a/src/bids_model/addConfoundsToDesignMatrix.m b/src/bids_model/addConfoundsToDesignMatrix.m
@@ -4,8 +4,7 @@
   %
   % This will update the design matrix of the root node of the model.
   %
-  % Similar to the module
-  % https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html
+  % Similar to the :func:`nilearn.interfaces.fmriprep.load_confounds`
   %
   % USAGE::
   %