Merge branch 'master' of https://github.com/AmoghJohri/TVB-Tests

rsHRF_Mediated_Brain_Dynamics.ipynb

@@ -4,10 +4,10 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Modeling Brain Dynamics Using the Virtual Brain (Using Individual Region-Specific HRF)\n",
+    "# Modeling fMRI BOLD signal dynamics with the Virtual Brain using the Individual Region-Specific HRF)\n",
     "\n",
-    "This study is along similar lines of the one at, https://github.com/mlion0200/educase_TVB_braintumor. \n",
-    "However, here we represent the effect of incorporating Individual Region-Specific HRF. The TVB BOLD simulation considers a constant HRF throughout the connectome of an individual, and across individuals. This reduces the specificity of the model. In the present study, we intend to personalize the models to a greater depth by retrieving the HRF for each connectome (and each region of the connectome) through the empericical BOLD time-series.\n",
+    "This notebook illustrates the workflow for creating a virtual brain similar to https://github.com/mlion0200/educase_TVB_braintumor. \n",
+    "However, here we investigate the effect of incorporating the Individual Region-Specific HRF instead of the standard model for the HRF. The TVB BOLD simulation considers a constant HRF for all the regions of the parcellation, and across individuals. This reduces the specificity of the model. In the present study, we intend to personalize the models to a greater depth by retrieving the local HRF for each empirical recording.\n",
     "The relevant additions to the TVB can be found at https://github.com/AmoghJohri/tvb-root/tree/amogh."
    ]
   },
@@ -72,14 +72,14 @@
    "metadata": {},
    "source": [
     "## Hemodynamic Response Function Retrieval\n",
-    "Instead of using a constant HRF, we retrieve the same through empirical region-wise BOLD time-series data(separately for each subject, and each brain region of the subject). For more information, visit: https://www.nitrc.org/projects/rshrf.\n",
+    "Instead of using a constant HRF, we retrieve the same through empirical region-wise BOLD time-series data (separately for each subject, and each brain region of the subject). For more information, visit: https://www.nitrc.org/projects/rshrf.\n",
     "\n",
     "<hr style=\"border:2px solid gray\"> </hr>\n",
     "\n",
     "![Resting-State HRF Retrieval](https://guorongwu.github.io/HRF/deconv.jpg)\n",
     "\n",
     "<hr style=\"border:2px solid gray\"> </hr>\n",
-    "Here, we carry out the steps 1 and 2 as shown in the figure. The region-wise emperical time-series forms the input and the HRF is retrieved from the same. The consequent BOLD simulations are then mediated through the retrieved HRF."
+    "Here, we carry out the steps 1 and 2 as shown in the figure. The region-wise empirical time-series forms the input and the HRF is retrieved from the same. The consequent neural simulations are then converted to BOLD through the retrieved HRF and downsampling"
    ]
   },
   {