From 6dbae9056a9fb71ca5ea85a9c200eb901d60a938 Mon Sep 17 00:00:00 2001
From: Anas Magdy <113242473+Mag-D-Anas@users.noreply.github.com>
Date: Thu, 3 Apr 2025 15:17:32 +0200
Subject: [PATCH 1/3] fix: adding "!" before pip3 in installation cell, adding
 zenode_get to the required packages

---
 ...tion_github_and_IVIM_Analysis_using_Python.ipynb | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb b/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
index a9bf1e0..ff82f40 100644
--- a/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
+++ b/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
@@ -45,7 +45,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "56273b2a",
    "metadata": {},
    "outputs": [
@@ -60,10 +60,11 @@
    ],
    "source": [
     "# install packages through anaconda prompt\n",
-    "pip3 install numpy\n",
-    "pip3 install matplotlib\n",
-    "pip3 install scipy\n",
-    "pip3 install nibabel"
+    "!pip3 install numpy\n",
+    "!pip3 install matplotlib\n",
+    "!pip3 install scipy\n",
+    "!pip3 install nibabel\n",
+    "!pip3 install zenodo_get"
    ]
   },
   {
@@ -76,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "9654f12d-6cfc-4639-884e-d7f2b23fa59f",
    "metadata": {},
    "outputs": [],

From 5cd8a7dcfcd58e1015a08fad504897ba9634ce86 Mon Sep 17 00:00:00 2001
From: Anas Magdy <113242473+Mag-D-Anas@users.noreply.github.com>
Date: Thu, 3 Apr 2025 15:19:30 +0200
Subject: [PATCH 2/3] fix: clearing output messages

---
 ...ection_github_and_IVIM_Analysis_using_Python.ipynb | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb b/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
index ff82f40..3bc9ce0 100644
--- a/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
+++ b/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
@@ -48,16 +48,7 @@
    "execution_count": null,
    "id": "56273b2a",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "SyntaxError",
-     "evalue": "invalid syntax (882689640.py, line 2)",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[1;36m  Cell \u001b[1;32mIn[3], line 2\u001b[1;36m\u001b[0m\n\u001b[1;33m    pip3 install numpy\u001b[0m\n\u001b[1;37m         ^\u001b[0m\n\u001b[1;31mSyntaxError\u001b[0m\u001b[1;31m:\u001b[0m invalid syntax\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# install packages through anaconda prompt\n",
     "!pip3 install numpy\n",

From addeb282b7479100aa0f152f61479bbd0cc16d7d Mon Sep 17 00:00:00 2001
From: Anas Magdy <113242473+Mag-D-Anas@users.noreply.github.com>
Date: Thu, 3 Apr 2025 16:26:58 +0200
Subject: [PATCH 3/3] doc: fixing another cell

---
 ...deCollection_github_and_IVIM_Analysis_using_Python.ipynb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb b/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
index 3bc9ce0..dc4de48 100644
--- a/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
+++ b/doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
@@ -406,9 +406,9 @@
    "outputs": [],
    "source": [
     "# install packages through anaconda prompt\n",
-    "pip3 install tqdm\n",
-    "pip3 install dipy\n",
-    "pip3 install joblib"
+    "!pip3 install tqdm\n",
+    "!pip3 install dipy\n",
+    "!pip3 install joblib"
    ]
   },
   {