deploy: d205e80

_sources/content/RSA.ipynb

@@ -138,10 +138,10 @@
    "source": [
     "sub = 'S01'\n",
     "\n",
-    "file_list = glob.glob(os.path.join(data_dir, 'derivatives','fmriprep', f'sub-{sub}' ,'func','*denoised*.nii.gz'))\n",
-    "file_list = [x for x in file_list if 'betas' not in x]\n",
+    "file_list = glob.glob(os.path.join(data_dir, 'derivatives', 'betas', f'{sub}*'))\n",
+    "file_list = [x for x in file_list if f'{sub}_betas.nii.gz' not in x]\n",
     "file_list.sort()\n",
-    "conditions = [os.path.basename(x).split(f'sub-{sub}_')[1].split('_denoised')[0] for x in file_list]\n",
+    "conditions = [os.path.basename(x).split(f'{sub}_beta_')[1].split('.nii.gz')[0] for x in file_list]\n",
     "beta = Brain_Data(file_list)"
    ]
   },
@@ -179,7 +179,7 @@
     }
    ],
    "source": [
-    "mask = Brain_Data(os.path.join('..', 'masks', 'k50_2mm.nii.gz'))\n",
+    "mask = Brain_Data('https://neurovault.org/media/images/8423/k50_2mm.nii.gz')\n",
     "mask_x = expand_mask(mask)\n",
     "\n",
     "mask.plot()"
@@ -815,7 +815,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.12.2"
   },
   "toc": {
    "base_numbering": 1,

content/RSA.html

@@ -607,10 +607,10 @@ <h3>Single Subject Pattern Similarity<a class="headerlink" href="#single-subject
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">sub</span> <span class="o">=</span> <span class="s1">&#39;S01&#39;</span>
 
-<span class="n">file_list</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">data_dir</span><span class="p">,</span> <span class="s1">&#39;derivatives&#39;</span><span class="p">,</span><span class="s1">&#39;fmriprep&#39;</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;sub-</span><span class="si">{</span><span class="n">sub</span><span class="si">}</span><span class="s1">&#39;</span> <span class="p">,</span><span class="s1">&#39;func&#39;</span><span class="p">,</span><span class="s1">&#39;*denoised*.nii.gz&#39;</span><span class="p">))</span>
-<span class="n">file_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">file_list</span> <span class="k">if</span> <span class="s1">&#39;betas&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">x</span><span class="p">]</span>
+<span class="n">file_list</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">data_dir</span><span class="p">,</span> <span class="s1">&#39;derivatives&#39;</span><span class="p">,</span> <span class="s1">&#39;betas&#39;</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">sub</span><span class="si">}</span><span class="s1">*&#39;</span><span class="p">))</span>
+<span class="n">file_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">file_list</span> <span class="k">if</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">sub</span><span class="si">}</span><span class="s1">_betas.nii.gz&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">x</span><span class="p">]</span>
 <span class="n">file_list</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
-<span class="n">conditions</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;sub-</span><span class="si">{</span><span class="n">sub</span><span class="si">}</span><span class="s1">_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_denoised&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">file_list</span><span class="p">]</span>
+<span class="n">conditions</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">sub</span><span class="si">}</span><span class="s1">_beta_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.nii.gz&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">file_list</span><span class="p">]</span>
 <span class="n">beta</span> <span class="o">=</span> <span class="n">Brain_Data</span><span class="p">(</span><span class="n">file_list</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -620,7 +620,7 @@ <h3>Single Subject Pattern Similarity<a class="headerlink" href="#single-subject
 <p>Let’s load our parcellation mask so that we can examine the pattern similarity across these conditions for each ROI.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">mask</span> <span class="o">=</span> <span class="n">Brain_Data</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;..&#39;</span><span class="p">,</span> <span class="s1">&#39;masks&#39;</span><span class="p">,</span> <span class="s1">&#39;k50_2mm.nii.gz&#39;</span><span class="p">))</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">mask</span> <span class="o">=</span> <span class="n">Brain_Data</span><span class="p">(</span><span class="s1">&#39;https://neurovault.org/media/images/8423/k50_2mm.nii.gz&#39;</span><span class="p">)</span>
 <span class="n">mask_x</span> <span class="o">=</span> <span class="n">expand_mask</span><span class="p">(</span><span class="n">mask</span><span class="p">)</span>
 
 <span class="n">mask</span><span class="o">.</span><span class="n">plot</span><span class="p">()</span>

content/Signal_Processing.html

@@ -767,7 +767,7 @@ <h3>Convolution<a class="headerlink" href="#convolution" title="Permalink to thi
 <img alt="../_images/3d8354983621059ebb04b1e2bb381446839db1374a04a52aeebe4e6a8b4e6514.png" src="../_images/3d8354983621059ebb04b1e2bb381446839db1374a04a52aeebe4e6a8b4e6514.png" />
 </div>
 </div>
-<p>For this example, we oversampled the function to make it more smooth.  In practice we will want to make sure that the kernel is the correct shape given our sampling resolution.  Be sure to se the oversampling to 1.  Notice how the function looks more jagged now?</p>
+<p>For this example, we oversampled the function to make it more smooth.  In practice we will want to make sure that the kernel is the correct shape given our sampling resolution.  Be sure to set the oversampling to 1.  Notice how the function looks more jagged now?</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">hrf</span> <span class="o">=</span> <span class="n">glover_hrf</span><span class="p">(</span><span class="n">tr</span><span class="p">,</span> <span class="n">oversampling</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>