Merge pull request #52 from neurorepro/iquant

Add cortical thickness stat analysis
carpentries-incubator · Jun 4, 2021 · bbab0f7 · bbab0f7
2 parents f59d52a + fe1fbf7
commit bbab0f7
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diff --git a/code/4_sMRI_segmentation_parcellation.ipynb b/code/4_sMRI_segmentation_parcellation.ipynb
@@ -7,7 +7,9 @@
     "# Lesson 4: sMRI Segmentation / Parcellation\n",
     "\n",
     "## Objectives\n",
-    "\n",
+    "- Understand and visualize tissue segmentation\n",
+    "- Manipulate atlases to extract regions of interests\n",
+    "- Visualize and interact with both volumetric and surface data\n",
     "\n",
     "## Python Requirements\n",
     "- numpy\n",
@@ -606,7 +608,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "##### Exercise: can you modify the code above to plot the intensity distribution before skull-stripping ? "
+    "##### Challenge: can you modify the code above to plot the intensity distribution before skull-stripping ? "
    ]
   },
   {
@@ -883,7 +885,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "##### Exercise: can you modify the code above to plot the white matter surface ? "
+    "##### Challenge: can you modify the code above to plot the white matter surface ? "
    ]
   },
   {

diff --git a/code/6_sMRI_quantification_stats.ipynb b/code/6_sMRI_quantification_stats.ipynb
diff --git a/episodes/06-Statistical_Analysis.md b/episodes/06-Statistical_Analysis.md
diff --git a/fig/episode_6/5_All_FSL.png b/fig/episode_6/5_All_FSL.png
diff --git a/fig/episode_6/5_CTchanges_SCZexercise_Bi.png b/fig/episode_6/5_CTchanges_SCZexercise_Bi.png
diff --git a/fig/episode_6/5_CorticalThickness_Img1.png b/fig/episode_6/5_CorticalThickness_Img1.png
diff --git a/fig/episode_6/5_EffectSize.png b/fig/episode_6/5_EffectSize.png
diff --git a/fig/episode_6/5_Fig1_corAtlas_AAL.png b/fig/episode_6/5_Fig1_corAtlas_AAL.png
diff --git a/fig/episode_6/5_Fig2_corAtlas_Schaefer.png b/fig/episode_6/5_Fig2_corAtlas_Schaefer.png
diff --git a/fig/episode_6/5_Fig3_corAtlas_Harvard-Oxford.png b/fig/episode_6/5_Fig3_corAtlas_Harvard-Oxford.png
diff --git a/fig/episode_6/5_Fig4_corAtlas_Destrieux.png b/fig/episode_6/5_Fig4_corAtlas_Destrieux.png
diff --git a/fig/episode_6/5_Fig5_subAtlas_Pauli.png b/fig/episode_6/5_Fig5_subAtlas_Pauli.png
diff --git a/fig/episode_6/5_HippL_FSL.png b/fig/episode_6/5_HippL_FSL.png
diff --git a/fig/episode_6/5_HippocampalSubfields.png b/fig/episode_6/5_HippocampalSubfields.png
diff --git a/fig/episode_6/5_MAGeTOverview.png b/fig/episode_6/5_MAGeTOverview.png
diff --git a/fig/episode_6/5_MeanCT_forGroups_A.png b/fig/episode_6/5_MeanCT_forGroups_A.png
diff --git a/fig/episode_6/5_SubVolumes.png b/fig/episode_6/5_SubVolumes.png
diff --git a/fig/episode_6/5_SubVolumes_All.png b/fig/episode_6/5_SubVolumes_All.png
diff --git a/fig/episode_6/5_VBM_OASIS_Eg.png b/fig/episode_6/5_VBM_OASIS_Eg.png
diff --git a/fig/episode_6/5_VBM_PP_DARTELinput.png b/fig/episode_6/5_VBM_PP_DARTELinput.png
diff --git a/fig/episode_6/5_VBM_PP_NewSeg.png b/fig/episode_6/5_VBM_PP_NewSeg.png
diff --git a/fig/episode_6/5_VBM_PP_norm2mni_OP.png b/fig/episode_6/5_VBM_PP_norm2mni_OP.png
diff --git a/fig/episode_6/5_VolAnalysis_Eg1.png b/fig/episode_6/5_VolAnalysis_Eg1.png
diff --git a/fig/episode_6/5_VolAnalysis_Eg2.png b/fig/episode_6/5_VolAnalysis_Eg2.png
diff --git a/fig/episode_6/ct_age_pvals.png b/fig/episode_6/ct_age_pvals.png
diff --git a/fig/episode_6/ct_age_r2.png b/fig/episode_6/ct_age_r2.png
diff --git a/fig/episode_6/ct_age_tvals_left_hemi.png b/fig/episode_6/ct_age_tvals_left_hemi.png
diff --git a/fig/episode_6/ct_age_tvals_right_hemi.png b/fig/episode_6/ct_age_tvals_right_hemi.png
diff --git a/fig/episode_6/group_cortical_thickness_boxplot.png b/fig/episode_6/group_cortical_thickness_boxplot.png
diff --git a/fig/episode_6/right_caudate_ROI.png b/fig/episode_6/right_caudate_ROI.png
diff --git a/fig/episode_6/roi_thickness_age.png b/fig/episode_6/roi_thickness_age.png
diff --git a/fig/episode_6/subject_cortical_thickness_mesh.png b/fig/episode_6/subject_cortical_thickness_mesh.png