Day 7 pages

issa-garcia · Mar 1, 2022 · 0dcbf5c · 0dcbf5c
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Showing 7 changed files with 28 additions and 131 deletions.
diff --git a/_config.yml b/_config.yml
@@ -69,12 +69,9 @@ exclude_patterns:
   - pages/markdown.md
   - pages/mentors.md
   - pages/methods_vs_functions.Rmd
-  - pages/model_one_voxel.Rmd
   - pages/multi_model_homework.md
-  - pages/multi_multiply.Rmd
   - pages/nans.md
   - pages/newaxis.Rmd
-  - pages/non_tr_onsets.Rmd
   - pages/numpy_diag.Rmd
   - pages/numpy_meshgrid.Rmd
   - pages/numpy_random.Rmd
@@ -99,7 +96,6 @@ exclude_patterns:
   - pages/subplots.Rmd
   - pages/subtract_mean_math.md
   - pages/subtract_means.Rmd
-  - pages/test_one_voxel.Rmd
   - pages/topics.md
   - pages/tr_and_headers.Rmd
   - pages/two_dunders.md

diff --git a/_toc.yml b/_toc.yml
@@ -33,6 +33,10 @@ parts:
 - caption: Hemodynamic response modeling
   chapters:
   - file: pages/convolution_background
+  - file: pages/model_one_voxel
+  - file: pages/test_one_voxel
+  - file: pages/multi_multiply
+  - file: pages/non_tr_onsets
 - caption: Code organization and collaboration
   chapters:
   # - file: pages/git_walk_through

diff --git a/pages/model_one_voxel.Rmd b/pages/model_one_voxel.Rmd
@@ -6,11 +6,13 @@ jupyter:
       format_name: rmarkdown
       format_version: '1.2'
       jupytext_version: 1.11.5
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
 ---
 
-$\newcommand{L}[1]{\| #1 \|}\newcommand{VL}[1]{\L{ \vec{#1} }}\newcommand{R}[1]{\operatorname{Re}\,(#1)}\newcommand{I}[1]{\operatorname{Im}\, (#1)}$
-
-## Modeling a single voxel
+# Modeling a single voxel
 
 Earlier – Voxel time courses – we were looking at a single voxel
 time course.
@@ -30,7 +32,7 @@ we discovered in First go at brain activation exercise:
 
 ```{python}
 img = nib.load('ds114_sub009_t2r1.nii')
-data = img.get_data()
+data = img.get_fdata()
 data = data[..., 4:]
 ```
 
@@ -116,31 +118,3 @@ print(np.sum(e_vec ** 2))
 plt.plot(voxel_time_course)
 plt.plot(y_hat)
 ```
-
-<!-- vim:ft=rst -->
-<!-- Course -->
-<!-- BIC -->
-<!-- Python distributions -->
-<!-- Version control -->
-<!-- Editors -->
-<!-- Python and common libraries -->
-<!-- IPython -->
-<!-- Virtualenv and helpers -->
-<!-- Pypi and packaging -->
-<!-- Mac development -->
-<!-- Windows development -->
-<!-- Nipy and friends -->
-<!-- FMRI datasets -->
-<!-- Languages -->
-<!-- Imaging software -->
-<!-- Installation -->
-<!-- Tutorials -->
-<!-- MB tutorials -->
-<!-- Ideas -->
-<!-- Psych-214 -->
-<!-- People -->
-<!-- Licenses -->
-<!-- Neuroimaging stuff -->
-<!-- OpenFMRI projects -->
-<!-- Unix -->
-<!-- Substitutions -->
diff --git a/pages/multi_multiply.Rmd b/pages/multi_multiply.Rmd
@@ -6,11 +6,13 @@ jupyter:
       format_name: rmarkdown
       format_version: '1.2'
       jupytext_version: 1.11.5
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
 ---
 
-$\newcommand{L}[1]{\| #1 \|}\newcommand{VL}[1]{\L{ \vec{#1} }}\newcommand{R}[1]{\operatorname{Re}\,(#1)}\newcommand{I}[1]{\operatorname{Im}\, (#1)}$
-
-## Estimation for many voxels at the same time
+# Estimation for many voxels at the same time
 
 We often want to fit the same design to many different voxels.
 
@@ -66,31 +68,3 @@ betas
 ```
 
 Of course this is true for any number of columns of Y.
-
-<!-- vim:ft=rst -->
-<!-- Course -->
-<!-- BIC -->
-<!-- Python distributions -->
-<!-- Version control -->
-<!-- Editors -->
-<!-- Python and common libraries -->
-<!-- IPython -->
-<!-- Virtualenv and helpers -->
-<!-- Pypi and packaging -->
-<!-- Mac development -->
-<!-- Windows development -->
-<!-- Nipy and friends -->
-<!-- FMRI datasets -->
-<!-- Languages -->
-<!-- Imaging software -->
-<!-- Installation -->
-<!-- Tutorials -->
-<!-- MB tutorials -->
-<!-- Ideas -->
-<!-- Psych-214 -->
-<!-- People -->
-<!-- Licenses -->
-<!-- Neuroimaging stuff -->
-<!-- OpenFMRI projects -->
-<!-- Unix -->
-<!-- Substitutions -->
diff --git a/pages/new_cond.txt b/pages/new_cond.txt
@@ -0,0 +1 @@
+../data/new_cond.txt
diff --git a/pages/non_tr_onsets.Rmd b/pages/non_tr_onsets.Rmd
@@ -6,11 +6,13 @@ jupyter:
       format_name: rmarkdown
       format_version: '1.2'
       jupytext_version: 1.11.5
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
 ---
 
-$\newcommand{L}[1]{\| #1 \|}\newcommand{VL}[1]{\L{ \vec{#1} }}\newcommand{R}[1]{\operatorname{Re}\,(#1)}\newcommand{I}[1]{\operatorname{Im}\, (#1)}$
-
-## Using onsets that do not start on a TR
+# Using onsets that do not start on a TR
 
 You’ll need the file `new_cond.txt` to type along with this
 demonstration.
@@ -184,31 +186,3 @@ plt.plot(tr_times[:20], tr_hemo[:20], 'x:')
 plt.xlabel('Time (seconds)')
 plt.ylabel('Convolved values at TR onsets')
 ```
-
-<!-- vim:ft=rst -->
-<!-- Course -->
-<!-- BIC -->
-<!-- Python distributions -->
-<!-- Version control -->
-<!-- Editors -->
-<!-- Python and common libraries -->
-<!-- IPython -->
-<!-- Virtualenv and helpers -->
-<!-- Pypi and packaging -->
-<!-- Mac development -->
-<!-- Windows development -->
-<!-- Nipy and friends -->
-<!-- FMRI datasets -->
-<!-- Languages -->
-<!-- Imaging software -->
-<!-- Installation -->
-<!-- Tutorials -->
-<!-- MB tutorials -->
-<!-- Ideas -->
-<!-- Psych-214 -->
-<!-- People -->
-<!-- Licenses -->
-<!-- Neuroimaging stuff -->
-<!-- OpenFMRI projects -->
-<!-- Unix -->
-<!-- Substitutions -->
diff --git a/pages/test_one_voxel.Rmd b/pages/test_one_voxel.Rmd
@@ -6,11 +6,13 @@ jupyter:
       format_name: rmarkdown
       format_version: '1.2'
       jupytext_version: 1.11.5
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
 ---
 
-$\newcommand{L}[1]{\| #1 \|}\newcommand{VL}[1]{\L{ \vec{#1} }}\newcommand{R}[1]{\operatorname{Re}\,(#1)}\newcommand{I}[1]{\operatorname{Im}\, (#1)}$
-
-## Testing a single voxel
+# Testing a single voxel
 
 A short ago (Modeling a single voxel), we were modeling a single voxel time
 course.
@@ -27,7 +29,7 @@ np.set_printoptions(precision=4)
 ```{python}
 import nibabel as nib
 img = nib.load('ds114_sub009_t2r1.nii')
-data = img.get_data()
+data = img.get_fdata()
 data = data[..., 4:]
 ```
 
@@ -155,7 +157,7 @@ p = 1 - ltp # upper tail p
 p
 ```
 
-## Compare our manual estimation to R
+# Compare our manual estimation to R
 
 Finally let’s save the voxel time course for us to compare this analysis to
 the `lm` estimation in R:
@@ -178,31 +180,3 @@ convolved = convolved[-(1:4)]
 res = lm(voxels ~ convolved)
 print(summary(res))
 ```
-
-<!-- vim:ft=rst -->
-<!-- Course -->
-<!-- BIC -->
-<!-- Python distributions -->
-<!-- Version control -->
-<!-- Editors -->
-<!-- Python and common libraries -->
-<!-- IPython -->
-<!-- Virtualenv and helpers -->
-<!-- Pypi and packaging -->
-<!-- Mac development -->
-<!-- Windows development -->
-<!-- Nipy and friends -->
-<!-- FMRI datasets -->
-<!-- Languages -->
-<!-- Imaging software -->
-<!-- Installation -->
-<!-- Tutorials -->
-<!-- MB tutorials -->
-<!-- Ideas -->
-<!-- Psych-214 -->
-<!-- People -->
-<!-- Licenses -->
-<!-- Neuroimaging stuff -->
-<!-- OpenFMRI projects -->
-<!-- Unix -->
-<!-- Substitutions -->