From 95897d9cb997c025a244a0e6eb832f664be4fef2 Mon Sep 17 00:00:00 2001
From: thibaultdvx <154365476+thibaultdvx@users.noreply.github.com>
Date: Thu, 30 May 2024 13:09:42 +0200
Subject: [PATCH] Update notebooks (#45)

---
 notebooks/generate.ipynb                |  52 +++++------
 notebooks/inference.ipynb               |  40 ++++-----
 notebooks/interpretability.ipynb        |  40 ++++-----
 notebooks/label_extraction.ipynb        | 112 ++++++++++++------------
 notebooks/preprocessing.ipynb           | 102 ++++++++++-----------
 notebooks/random_search.ipynb           |  42 ++++-----
 notebooks/training.ipynb                |  72 +++++++--------
 notebooks/training_classification.ipynb |  84 +++++++++---------
 notebooks/training_reconstruction.ipynb |  78 ++++++++---------
 notebooks/training_regression.ipynb     |  62 ++++++-------
 10 files changed, 342 insertions(+), 342 deletions(-)

diff --git a/notebooks/generate.ipynb b/notebooks/generate.ipynb
index 15316c1..382a2fb 100644
--- a/notebooks/generate.ipynb
+++ b/notebooks/generate.ipynb
@@ -3,17 +3,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "98e2c0cc",
+   "id": "6b249afa",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "6535c01d",
+   "id": "6a516f13",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -43,19 +43,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "47318d40",
+   "id": "3a1b7f1d",
    "metadata": {
     "lines_to_next_cell": 0
    },
    "outputs": [],
    "source": [
-    "!curl -k https://aramislab.paris.inria.fr/clinicadl/files/data/handbook_2023/data_oasis/CAPS_example.tar.gz -o oasisCaps.tar.gz\n",
+    "!curl -k https://aramislab.paris.inria.fr/clinicadl/files/handbook_2023/data_oasis/CAPS_example.tar.gz -o oasisCaps.tar.gz\n",
     "!tar xf oasisCaps.tar.gz"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "ae43371d",
+   "id": "5737c2cc",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -101,7 +101,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24375018",
+   "id": "2978c583",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -112,7 +112,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a16e3639",
+   "id": "ff2a5926",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -127,7 +127,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "db02b1ea",
+   "id": "fd8651a4",
    "metadata": {},
    "source": [
     "#### Get the labels AD and CN\n",
@@ -140,7 +140,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "56525e32",
+   "id": "68d3a21d",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -153,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7e5a6729",
+   "id": "3018c01a",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -166,7 +166,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9abb1c9a",
+   "id": "34eea13c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -178,7 +178,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "22a6fe39",
+   "id": "6ac39bfd",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -201,7 +201,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4f4ad49b",
+   "id": "70ade2f2",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -212,7 +212,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6eba2f26",
+   "id": "51b695b2",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -224,7 +224,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fb7308dc",
+   "id": "d5b4707b",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -243,7 +243,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d5ba6a82",
+   "id": "8b7780cd",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -255,7 +255,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bd122070",
+   "id": "cb3bed6f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -268,7 +268,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14e0cdee",
+   "id": "6199da50",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -281,7 +281,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f617fd3b",
+   "id": "204ac99a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -299,7 +299,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b9af9c02",
+   "id": "92075683",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -335,7 +335,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fcf4cb72",
+   "id": "6dd2bf6c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -344,7 +344,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7a49d044",
+   "id": "51bd7a07",
    "metadata": {},
    "source": [
     "The command generates 3D images of same size as the input images formatted as\n",
@@ -355,7 +355,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3e241670",
+   "id": "f7de8d12",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -389,7 +389,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4ed71edc",
+   "id": "d4d834f0",
    "metadata": {},
    "source": [
     "### Running the task\n",
@@ -403,7 +403,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9991f499",
+   "id": "fddc70be",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/notebooks/inference.ipynb b/notebooks/inference.ipynb
index bc615db..90de8a7 100644
--- a/notebooks/inference.ipynb
+++ b/notebooks/inference.ipynb
@@ -3,19 +3,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "43d1cf22",
+   "id": "05baad6c",
    "metadata": {
     "lines_to_next_cell": 0
    },
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "e282e32d",
+   "id": "926641e6",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -84,7 +84,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c37c9b9e",
+   "id": "72dfbf7c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -110,7 +110,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c3c68ac5",
+   "id": "9235964f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -135,7 +135,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "75ff167a",
+   "id": "0388f991",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -156,7 +156,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e184e78b",
+   "id": "5b1e59cf",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -170,7 +170,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6db943f4",
+   "id": "41ebad1a",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -194,7 +194,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6ede8598",
+   "id": "21722da5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -205,7 +205,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4ab97fd1",
+   "id": "1549ae37",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -216,7 +216,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d9a61f55",
+   "id": "9dc0a014",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -227,7 +227,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8b210854",
+   "id": "e369c517",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -240,7 +240,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "23bb45a7",
+   "id": "e66c5960",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -251,7 +251,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3d79d636",
+   "id": "ce67c0b5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -265,7 +265,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f4a81ec1",
+   "id": "a2b3f78b",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -282,7 +282,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1b5a09f0",
+   "id": "0b76c2eb",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -294,7 +294,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d61210cc",
+   "id": "48fab235",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -305,7 +305,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "eac273dd",
+   "id": "830744c4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -321,7 +321,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9f28bd8e",
+   "id": "2b501d3e",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -337,7 +337,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f3adfb4f",
+   "id": "9d233554",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/notebooks/interpretability.ipynb b/notebooks/interpretability.ipynb
index fb07aff..2095c53 100644
--- a/notebooks/interpretability.ipynb
+++ b/notebooks/interpretability.ipynb
@@ -3,19 +3,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e0505734",
+   "id": "297afdc9",
    "metadata": {
     "lines_to_next_cell": 0
    },
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "84bd10aa",
+   "id": "ab2a5c26",
    "metadata": {},
    "source": [
     "# Generate saliency maps on trained networks\n",
@@ -38,7 +38,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f7aa21c0",
+   "id": "9d005d06",
    "metadata": {},
    "source": [
     "## Use of trivial datasets\n",
@@ -52,7 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "be87ea33",
+   "id": "da505234",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -64,7 +64,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "befaefe0",
+   "id": "fe6aa582",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -75,7 +75,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7a179e73",
+   "id": "328f4240",
    "metadata": {},
    "source": [
     "In this trivial dataset, \"AD\" brains are atrophied according to the first mask\n",
@@ -87,7 +87,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5e2c3539",
+   "id": "3c3462ad",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +100,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a44eac5e",
+   "id": "cceb3c3f",
    "metadata": {},
    "source": [
     "Saliency maps will be generated using trivial data generated from OASIS. If\n",
@@ -112,7 +112,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f8aabb20",
+   "id": "4e45cdc0",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -128,7 +128,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3d3d6aac",
+   "id": "70d4e259",
    "metadata": {},
    "source": [
     "# Generate individual saliency maps\n",
@@ -157,7 +157,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3ae956f5",
+   "id": "1ae111f2",
    "metadata": {},
    "source": [
     "In the following we chose to generate saliency map based on the opposite\n",
@@ -175,7 +175,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c998e4f1",
+   "id": "01c8d858",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -188,7 +188,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b5374af8",
+   "id": "b566aa5d",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -200,7 +200,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "89353f65",
+   "id": "771c64e5",
    "metadata": {},
    "source": [
     "This command will generate saliency maps for the model selected on validation \n",
@@ -215,7 +215,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7ba761e0",
+   "id": "d0f0cb5c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -224,7 +224,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8f0b351f",
+   "id": "5222d285",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -238,7 +238,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "87416c32",
+   "id": "fd574038",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -264,7 +264,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ca1f6d15",
+   "id": "b52ea5c1",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -277,7 +277,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9a805b07",
+   "id": "118d85d9",
    "metadata": {},
    "outputs": [],
    "source": []
diff --git a/notebooks/label_extraction.ipynb b/notebooks/label_extraction.ipynb
index dab72a9..599f41b 100644
--- a/notebooks/label_extraction.ipynb
+++ b/notebooks/label_extraction.ipynb
@@ -3,17 +3,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b2353959",
+   "id": "5f97905f",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Uncomment the next lines if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "d14d9104",
+   "id": "3905db98",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -35,7 +35,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5fe8c3f5",
+   "id": "e20db782",
    "metadata": {},
    "source": [
     "## Before starting\n",
@@ -51,32 +51,32 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d9e9fe9e",
+   "id": "090a5244",
    "metadata": {},
    "outputs": [],
    "source": [
     "# #OASIS BIDS\n",
-    "!curl -k https://aramislab.paris.inria.fr/files/data/handbook_2023/data_oasis/BIDS_example.tar.gz -o BIDS_example.tar.gz\n",
+    "!curl -k https://aramislab.paris.inria.fr/clinicadl/files/handbook_2023/data_oasis/BIDS_example.tar.gz -o BIDS_example.tar.gz\n",
     "!tar xf BIDS_example.tar.gz "
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "55ab43b6",
+   "id": "1eb7c0ab",
    "metadata": {
     "lines_to_next_cell": 2
    },
    "outputs": [],
    "source": [
     "# #ADNI BIDS\n",
-    "!curl -k https://aramislab.paris.inria.fr/files/data/handbook_2023/data_adni/BIDS_example.tar.gz -o BIDS_example.tar.gz\n",
+    "!curl -k https://aramislab.paris.inria.fr/clinicadl/files/handbook_2023/data_adni/BIDS_example.tar.gz -o BIDS_example.tar.gz\n",
     "!tar xf BIDS_example.tar.gz "
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "a4c73d62",
+   "id": "a05858a0",
    "metadata": {},
    "source": [
     "## Get metadata from a BIDS hierarchy with `clinica iotools`\n",
@@ -102,7 +102,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "cdf85436",
+   "id": "5c4cb2dd",
    "metadata": {},
    "source": [
     "We are going to run some experiments on the ADNI and OASIS datasets, \n",
@@ -115,7 +115,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8fe6cac7",
+   "id": "6eac395d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -126,7 +126,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2b8edc9e",
+   "id": "4e71aa68",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -137,7 +137,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ef5f166e",
+   "id": "25b0b153",
    "metadata": {},
    "source": [
     "### Check missing modalities for each subject\n",
@@ -163,7 +163,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "79b47f92",
+   "id": "cdca2e47",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -176,7 +176,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "846ee251",
+   "id": "4ce5d933",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -187,7 +187,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "35417aba",
+   "id": "00f4e094",
    "metadata": {},
    "source": [
     "The output of this command, `missing_mods/`, is a folder with a series of\n",
@@ -197,7 +197,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9a07d968",
+   "id": "529364dd",
    "metadata": {},
    "source": [
     "## Prepare metadata with `clinicadl tsvtools` \n",
@@ -219,7 +219,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "06b12749",
+   "id": "d1ac7ae0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -232,7 +232,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4899cea7",
+   "id": "be3e112b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -244,7 +244,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0af71c49",
+   "id": "28a481d1",
    "metadata": {},
    "source": [
     "### Get the labels\n",
@@ -273,7 +273,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "53482736",
+   "id": "2eb7d208",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -286,7 +286,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "261b4d37",
+   "id": "f69efd82",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -297,7 +297,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "14959fbb",
+   "id": "3f29c9bc",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -314,7 +314,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a9577db5",
+   "id": "a4c132af",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -325,7 +325,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1682021d",
+   "id": "71a0cf40",
    "metadata": {},
    "source": [
     "This tool writes a unique TSV file containing the labels asked by the user.\n",
@@ -344,7 +344,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4f9c33f0",
+   "id": "cfe53db1",
    "metadata": {},
    "source": [
     "### Analyze the population\n",
@@ -358,7 +358,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "dd03aba9",
+   "id": "fb45a198",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -384,7 +384,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "722d6071",
+   "id": "80b79883",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -393,7 +393,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ea422f74",
+   "id": "c7089a17",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -422,7 +422,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "76cbf250",
+   "id": "0f0923bc",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -435,7 +435,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "37ac519f",
+   "id": "5266375f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -446,7 +446,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4ce5ca3f",
+   "id": "330b476d",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -492,7 +492,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fe22b57a",
+   "id": "87ac17be",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -504,7 +504,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6c4d4bcc",
+   "id": "b9dbb64f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -515,7 +515,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b07c445f",
+   "id": "0e645e2b",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -531,7 +531,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7cd184e9",
+   "id": "84ff5107",
    "metadata": {},
    "source": [
     "There is no significant bias on age anymore, but do you notice any other\n",
@@ -552,7 +552,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c6e0e680",
+   "id": "1d726d1e",
    "metadata": {},
    "source": [
     "### Get the progression of the Alzheimer's disease\n",
@@ -591,7 +591,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f3959685",
+   "id": "48342788",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -602,7 +602,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "73569dcb",
+   "id": "61eab36d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -612,7 +612,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fcddbbfe",
+   "id": "6375b6b8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -624,7 +624,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2885fc5c",
+   "id": "071dadb4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -685,7 +685,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e9ccf08e",
+   "id": "c6ab7f38",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -695,7 +695,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1eea0f3f",
+   "id": "6abeb5fe",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -707,7 +707,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "69ac5b7f",
+   "id": "55070732",
    "metadata": {},
    "source": [
     "The differences between the populations of the train + validation and test \n",
@@ -718,7 +718,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5ef425c7",
+   "id": "6d7c3c48",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -730,7 +730,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c9d13a14",
+   "id": "e5e8d35d",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -742,7 +742,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7f0bba8b",
+   "id": "5d3dad40",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -756,7 +756,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0cdb43ca",
+   "id": "f8123d84",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -778,7 +778,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0a60ea4a",
+   "id": "656ca4a7",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -812,7 +812,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b8caa94d",
+   "id": "bca6146b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -822,7 +822,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d148346c",
+   "id": "8cc98119",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -834,7 +834,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e53f436f",
+   "id": "22637121",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -863,7 +863,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "600f180f",
+   "id": "294a1bae",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -950,7 +950,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b5c11df2",
+   "id": "4fc968c4",
    "metadata": {},
    "source": [
     "If no Error was raised, then none of the three conditions was broken. It is now\n",
@@ -971,7 +971,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "990c7b70",
+   "id": "cacc0d0c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -983,7 +983,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f873881c",
+   "id": "6793c3f7",
    "metadata": {},
    "outputs": [],
    "source": []
diff --git a/notebooks/preprocessing.ipynb b/notebooks/preprocessing.ipynb
index 9f9a8bd..4b1e1e9 100644
--- a/notebooks/preprocessing.ipynb
+++ b/notebooks/preprocessing.ipynb
@@ -3,17 +3,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21197d4f",
+   "id": "93e0b753",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Uncomment the next line if running in Google Colab\n",
-    "# !pip install clinicadl==1.3.0"
+    "# !pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "545460bd",
+   "id": "bab86962",
    "metadata": {},
    "source": [
     "# Prepare your neuroimaging data\n",
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6ff9d1d9",
+   "id": "1229d82a",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -73,7 +73,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fb3d24d9",
+   "id": "18b701f3",
    "metadata": {},
    "source": [
     "\n",
@@ -103,7 +103,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "714b0c06",
+   "id": "60a812f6",
    "metadata": {},
    "source": [
     "### Before starting\n",
@@ -114,7 +114,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c964a259",
+   "id": "c26b3f0b",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -127,7 +127,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0b401f32",
+   "id": "acd05b37",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -139,7 +139,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "77aef766",
+   "id": "bcae68f5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -149,7 +149,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7e264314",
+   "id": "d31970af",
    "metadata": {},
    "source": [
     "\n",
@@ -161,7 +161,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a9e0767e",
+   "id": "87f8dab6",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -174,7 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6d2a5ccd",
+   "id": "1cc94c17",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -186,7 +186,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c0e9b892",
+   "id": "e37d40e4",
    "metadata": {},
    "source": [
     "# Why prepare data ?\n",
@@ -215,7 +215,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4c8bcedc",
+   "id": "f309a63e",
    "metadata": {},
    "source": [
     "\n",
@@ -241,7 +241,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3954e768",
+   "id": "f96b6d4b",
    "metadata": {},
    "source": [
     "This notebook presents three possible preprocessing steps using the [Clinica](https://www.clinica.run/doc/)\n",
@@ -254,7 +254,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0731a32d",
+   "id": "9e279250",
    "metadata": {},
    "source": [
     "<a id='preprocessing:t1-linear'></a>\n",
@@ -283,7 +283,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3ab3a606",
+   "id": "3b7c9e1f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -294,7 +294,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13dd7a71",
+   "id": "14dbe884",
    "metadata": {},
    "source": [
     "These steps can be run with this simple command line:\n",
@@ -311,7 +311,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1be4ed8b",
+   "id": "0f90c3cf",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -329,7 +329,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "de5c6ac7",
+   "id": "d44cafc1",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -340,7 +340,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a850ce36",
+   "id": "422f676e",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -351,7 +351,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "12b5e853",
+   "id": "315fe6b7",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -363,7 +363,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "21c5d89c",
+   "id": "82b43fe2",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -375,7 +375,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "286c5d95",
+   "id": "bd58ebc7",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -387,7 +387,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c9ef2a36",
+   "id": "9bc8035c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -403,7 +403,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "46d9174a",
+   "id": "3a9e9b9c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -415,7 +415,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2d2e6765",
+   "id": "3156cb3f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -438,7 +438,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5bf410ed",
+   "id": "a0834aeb",
    "metadata": {},
    "source": [
     "<a id='preprocessing:pet-linear'></a>\n",
@@ -458,7 +458,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d2b25f01",
+   "id": "f696178b",
    "metadata": {},
    "source": [
     "```{note}\n",
@@ -468,7 +468,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "65642a93",
+   "id": "1d4efd5a",
    "metadata": {},
    "source": [
     "The pipeline can be run with the following command line:\n",
@@ -496,7 +496,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a9d13f1d",
+   "id": "a8c2981a",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -514,7 +514,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "010bfca2",
+   "id": "70ef4ada",
    "metadata": {},
    "source": [
     "### Run the pipeline\n",
@@ -525,7 +525,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30360ff6",
+   "id": "fa8fb43d",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -538,7 +538,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9362e758",
+   "id": "b327de9e",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -550,7 +550,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "136b2b59",
+   "id": "3bb6b711",
    "metadata": {},
    "source": [
     "Once the pipeline has been run, the necessary outputs for the next steps are\n",
@@ -560,7 +560,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c217792b",
+   "id": "8e56c0cd",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -572,7 +572,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5fa87eee",
+   "id": "d753c89d",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -584,7 +584,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1ac96289",
+   "id": "779668b0",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -596,7 +596,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17a2ece2",
+   "id": "a4207824",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -619,7 +619,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "21ac492e",
+   "id": "fad40d63",
    "metadata": {},
    "source": [
     "# Quality check of your preprocessed data"
@@ -627,7 +627,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "56324764",
+   "id": "8908b2cb",
    "metadata": {},
    "source": [
     "From the 2 visualizations above, we can see that after the preprocessing, some\n",
@@ -644,7 +644,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1fdb08a9",
+   "id": "7a851a04",
    "metadata": {},
    "source": [
     "To automatically assess the quality of the **t1-linear** or the **pet-linear** preprocessing, we\n",
@@ -672,7 +672,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b0545ef5",
+   "id": "c6d4f301",
    "metadata": {},
    "source": [
     "```{note}\n",
@@ -684,7 +684,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8b2869e8",
+   "id": "75af0600",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -695,7 +695,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "01657786",
+   "id": "c6c69c1e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -706,7 +706,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2a717e12",
+   "id": "84f8aa87",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -716,7 +716,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3995c67b",
+   "id": "be6e8420",
    "metadata": {},
    "source": [
     "```{warning}\n",
@@ -729,7 +729,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0efe8e28",
+   "id": "8b134ba3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -740,7 +740,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fd9a1e0e",
+   "id": "2e6aa98b",
    "metadata": {},
    "source": [
     "Based on these TSV file, participant `OASIS10304` should be discarded for the\n",
@@ -753,7 +753,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6bf75569",
+   "id": "3b75fd90",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -764,7 +764,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e2a04432",
+   "id": "b37e1985",
    "metadata": {
     "lines_to_next_cell": 2
    },
diff --git a/notebooks/random_search.ipynb b/notebooks/random_search.ipynb
index 346a930..a621650 100644
--- a/notebooks/random_search.ipynb
+++ b/notebooks/random_search.ipynb
@@ -3,19 +3,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8c74ca91",
+   "id": "c9b870be",
    "metadata": {
     "lines_to_next_cell": 0
    },
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "c1b77e45",
+   "id": "3c6416a5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -43,18 +43,18 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a26d6985",
+   "id": "092236a7",
    "metadata": {},
    "outputs": [],
    "source": [
-    "!curl -k https://aramislab.paris.inria.fr/files/data/handbook_2023/data_oasis/CAPS_extracted.tar.gz -o oasisCaps.tar.gz\n",
+    "!curl -k https://aramislab.paris.inria.fr/clinicadl/files/handbook_2023/data_oasis/CAPS_extracted.tar.gz -o oasisCaps.tar.gz\n",
     "!tar xf oasisCaps.tar.gz"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "08dd369f",
+   "id": "1e2a3966",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -65,7 +65,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a71cd395",
+   "id": "b6fe0f4f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -89,7 +89,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "84f569ef",
+   "id": "9ca54f20",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -122,7 +122,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a40717b6",
+   "id": "4e3972d4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -159,7 +159,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b691ce65",
+   "id": "a841467e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -188,7 +188,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "69efc37c",
+   "id": "f30a9a2e",
    "metadata": {},
    "source": [
     "# Prerequisites\n",
@@ -204,7 +204,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b257108b",
+   "id": "3cb03c7c",
    "metadata": {},
    "source": [
     "# Running the task\n",
@@ -256,7 +256,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4216fcba",
+   "id": "306de0d4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -267,7 +267,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "622633fb",
+   "id": "14c93f18",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -280,7 +280,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d7cf2f7a",
+   "id": "f061d080",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -293,7 +293,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2ef9ebb2",
+   "id": "95302e54",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -313,7 +313,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "acdef25a",
+   "id": "eef847a5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -333,7 +333,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "445bf05a",
+   "id": "3959de77",
    "metadata": {},
    "source": [
     "One convolutional block is described by the following values:\n",
@@ -349,7 +349,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c4a911e2",
+   "id": "938479ac",
    "metadata": {},
    "source": [
     "### Convolutional block - example 1\n",
@@ -373,7 +373,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2277686e",
+   "id": "44378fed",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -404,7 +404,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b57352ac",
+   "id": "14424f88",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/notebooks/training.ipynb b/notebooks/training.ipynb
index ae22d8e..386005f 100644
--- a/notebooks/training.ipynb
+++ b/notebooks/training.ipynb
@@ -3,19 +3,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "07687ffd",
+   "id": "b1f2b712",
    "metadata": {
     "lines_to_next_cell": 0
    },
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "92be36e0",
+   "id": "03a36ddc",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -36,7 +36,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d25a5154",
+   "id": "0dff17a8",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -52,7 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "be7d0658",
+   "id": "808e0d05",
    "metadata": {
     "lines_to_next_cell": 0,
     "title": "[markwdown]"
@@ -76,7 +76,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2ec493e3",
+   "id": "f35c6631",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -156,7 +156,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b40acc20",
+   "id": "1371a563",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -205,7 +205,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6abd2255",
+   "id": "00519972",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -219,7 +219,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7aca0989",
+   "id": "fd0f04fc",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -233,7 +233,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bde03d22",
+   "id": "4f0bff8a",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -244,7 +244,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9cf724d5",
+   "id": "c5a198cb",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -320,7 +320,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "76a2b1ae",
+   "id": "7d83c6b4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -334,7 +334,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33739eaa",
+   "id": "c2159b78",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -348,7 +348,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "57e4a9d8",
+   "id": "a780bb5d",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -366,7 +366,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4c7faff6",
+   "id": "f8eb72ca",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -385,7 +385,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fdd5d9fa",
+   "id": "1099a9c3",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -402,7 +402,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23740462",
+   "id": "b12d9778",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -416,7 +416,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f81b19cb",
+   "id": "2bd98725",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -434,7 +434,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "016049c9",
+   "id": "2d7acb49",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -453,7 +453,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "92ebd2ca",
+   "id": "23f3ef3a",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -492,7 +492,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4e3b8469",
+   "id": "a7a8a64f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -506,7 +506,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "09982978",
+   "id": "733e317f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -523,7 +523,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "61964f5d",
+   "id": "26688170",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -587,7 +587,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "300e7514",
+   "id": "0947b42c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -602,7 +602,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6d1e51eb",
+   "id": "58c55d96",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -612,7 +612,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "114aad32",
+   "id": "9b19f82d",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -637,7 +637,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "803da3ba",
+   "id": "5eecd87e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -647,7 +647,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3ba7a910",
+   "id": "fe889ce3",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -660,7 +660,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "364f0f76",
+   "id": "b6932b2f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -674,7 +674,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "02ae76e9",
+   "id": "0824d0ec",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -703,7 +703,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23ba97e5",
+   "id": "37885557",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -714,7 +714,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "078f46ef",
+   "id": "544a605c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -725,7 +725,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0cf7712c",
+   "id": "580952d7",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -736,7 +736,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "373fffa4",
+   "id": "bb020d00",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -747,7 +747,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5f829302",
+   "id": "1ecad234",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -757,7 +757,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "259cc877",
+   "id": "d9da7e6d",
    "metadata": {},
    "outputs": [],
    "source": []
diff --git a/notebooks/training_classification.ipynb b/notebooks/training_classification.ipynb
index b180838..4777543 100644
--- a/notebooks/training_classification.ipynb
+++ b/notebooks/training_classification.ipynb
@@ -3,17 +3,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d7cc0e9e",
+   "id": "b69a7f7f",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "d88d11a5",
+   "id": "aab007d4",
    "metadata": {},
    "source": [
     "# Classification with a CNN on 2D slice\n",
@@ -47,7 +47,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b6ee3964",
+   "id": "017007cc",
    "metadata": {},
    "source": [
     "##  2D slice-level tensor extraction with the `prepare-data` pipeline\n",
@@ -66,7 +66,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "36b66112",
+   "id": "bb91495d",
    "metadata": {},
    "source": [
     "You need to run the following command line:\n",
@@ -88,7 +88,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "dae0cc82",
+   "id": "6a3842f5",
    "metadata": {},
    "source": [
     "Output files are stored into a new folder (inside the CAPS) and follows a\n",
@@ -119,7 +119,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "59517908",
+   "id": "2e5c0d20",
    "metadata": {},
    "source": [
     "In short, there is a folder for each feature (**image**, **slice**, **roi** or **patch**)\n",
@@ -140,7 +140,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8afe75f9",
+   "id": "980b9dc8",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -166,7 +166,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a658c564",
+   "id": "359a8bb3",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -180,7 +180,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d9a2ca13",
+   "id": "71086e22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -190,7 +190,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "af6447ec",
+   "id": "4c61e184",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -203,7 +203,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6d21191c",
+   "id": "73a5f856",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -214,7 +214,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "46dfbe4f",
+   "id": "56e8cac6",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -225,7 +225,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f618d903",
+   "id": "77d79286",
    "metadata": {},
    "source": [
     "At the end of this command, a new directory named `deeplearning_prepare_data`\n",
@@ -237,7 +237,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9d0e047a",
+   "id": "7e25a588",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -250,7 +250,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3c190557",
+   "id": "4b1970aa",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -259,7 +259,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "524a2cbd",
+   "id": "3ce02af0",
    "metadata": {},
    "source": [
     "# Train your own models\n",
@@ -276,7 +276,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "640cf991",
+   "id": "34f398dd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -288,7 +288,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a8e88ce3",
+   "id": "da6a03cf",
    "metadata": {},
    "source": [
     "\n",
@@ -306,7 +306,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c8644ec9",
+   "id": "6fc78011",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -322,7 +322,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6feeaeba",
+   "id": "afc072e5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -352,7 +352,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7c8cd2a5",
+   "id": "6c91e43f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -367,7 +367,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "62c37ef0",
+   "id": "8f15961c",
    "metadata": {},
    "source": [
     "### Running the task\n",
@@ -407,7 +407,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "34653d78",
+   "id": "c87359e0",
    "metadata": {},
    "source": [
     "A few options depend on the classification task:\n",
@@ -425,7 +425,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "78129c68",
+   "id": "0dafeb96",
    "metadata": {},
    "source": [
     "```{note}\n",
@@ -439,7 +439,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3c95b0e1",
+   "id": "1a5e369c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -450,7 +450,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8f3465c6",
+   "id": "e0e73e9d",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -465,7 +465,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "039dcf8d",
+   "id": "c7075e1b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -477,7 +477,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f03daf42",
+   "id": "9646cb6b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -487,7 +487,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b7eb498b",
+   "id": "96b20cef",
    "metadata": {},
    "source": [
     "The `clinicadl train` command outputs a MAPS structure in which there are only\n",
@@ -542,7 +542,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "393a246d",
+   "id": "86a4087e",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -555,7 +555,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4a4651a0",
+   "id": "034921d8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -566,7 +566,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "347a15bf",
+   "id": "85f0a372",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -576,7 +576,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f50a61ad",
+   "id": "280b4cdf",
    "metadata": {},
    "source": [
     "If you failed to train the model, you also need to download the TSV files with \n",
@@ -589,7 +589,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ed6813ac",
+   "id": "50b19197",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -599,7 +599,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6f141575",
+   "id": "702ddfbc",
    "metadata": {},
    "source": [
     "The `predict` functionality performs individual prediction and metrics\n",
@@ -611,7 +611,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5c0d6a0d",
+   "id": "d9b61b42",
    "metadata": {},
    "source": [
     "### Running the task \n",
@@ -640,7 +640,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b27490f6",
+   "id": "5c4526ef",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -651,7 +651,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "dd9623f1",
+   "id": "5624b5a4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -660,7 +660,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "122ba143",
+   "id": "f58757e9",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -689,7 +689,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "310c210c",
+   "id": "96793a96",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -703,7 +703,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6e709720",
+   "id": "00783676",
    "metadata": {},
    "outputs": [],
    "source": []
diff --git a/notebooks/training_reconstruction.ipynb b/notebooks/training_reconstruction.ipynb
index aeb7c0d..c1eb75f 100644
--- a/notebooks/training_reconstruction.ipynb
+++ b/notebooks/training_reconstruction.ipynb
@@ -3,17 +3,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "dc7ebb47",
+   "id": "4a899113",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "45248f5f",
+   "id": "f881cf8b",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -55,7 +55,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "cc831c84",
+   "id": "c129139b",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -76,7 +76,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6fcb41ee",
+   "id": "770cf607",
    "metadata": {},
    "source": [
     "##  3D patch-level tensor extraction with the `prepare-data` pipeline\n",
@@ -161,7 +161,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8d14dba3",
+   "id": "a3f382aa",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -173,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0ab11b73",
+   "id": "cf16b095",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -185,7 +185,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "285c67c9",
+   "id": "b427f11b",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -196,7 +196,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b41f166b",
+   "id": "4c91a087",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -207,7 +207,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fbfc0b98",
+   "id": "1146b556",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -219,7 +219,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "55b3e424",
+   "id": "0c317576",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -229,7 +229,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ce2157b9",
+   "id": "2521e2db",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -247,7 +247,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1e690e07",
+   "id": "faf37224",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -257,7 +257,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "92edbfbe",
+   "id": "e27cd581",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -274,7 +274,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5557be1e",
+   "id": "04d3e704",
    "metadata": {},
    "source": [
     "As for the 2D slice-level model, the gradient updates are done based on the\n",
@@ -305,7 +305,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7320fc03",
+   "id": "ecd4c355",
    "metadata": {},
    "source": [
     "## Before starting \n",
@@ -321,7 +321,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d3fe8821",
+   "id": "c8fb62a1",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -337,7 +337,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3f6257e4",
+   "id": "c56bf4bb",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -357,7 +357,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "59580cec",
+   "id": "a153194c",
    "metadata": {},
    "source": [
     "## `clinicadl train RECONSTRUCTION` \n",
@@ -371,7 +371,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "36598fca",
+   "id": "17d274b6",
    "metadata": {},
    "source": [
     "### Prerequisites\n",
@@ -383,7 +383,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "81c5a014",
+   "id": "e546a2ab",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -425,7 +425,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5bb3bc2a",
+   "id": "ad478cb3",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -440,7 +440,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8ba8804c",
+   "id": "0e6b1ed7",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -452,7 +452,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "64d25350",
+   "id": "bb8bd424",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -462,7 +462,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7c2ac389",
+   "id": "bbbf2d4c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -475,7 +475,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d9f76cd7",
+   "id": "0e424476",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -488,7 +488,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7db30855",
+   "id": "bca3fab4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -528,7 +528,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7478bdfe",
+   "id": "1a591cde",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -539,7 +539,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5c4c4036",
+   "id": "1aa8ee99",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -552,7 +552,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7598116a",
+   "id": "2a951a22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -562,7 +562,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "49e42f0b",
+   "id": "5dfcbc8a",
    "metadata": {},
    "source": [
     "The clinicadl train command outputs a MAPS structure in which there are only\n",
@@ -616,7 +616,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2538a07a",
+   "id": "15433f12",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -629,7 +629,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e224ffd1",
+   "id": "9921192f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -639,7 +639,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "40d2ca17",
+   "id": "c21f15c6",
    "metadata": {},
    "source": [
     "The `predict` functionality performs individual prediction and metrics\n",
@@ -651,7 +651,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "50cc3171",
+   "id": "ffd0fbeb",
    "metadata": {},
    "source": [
     "### Running the task \n",
@@ -688,7 +688,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32804029",
+   "id": "daf8ab94",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -699,7 +699,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34d8953c",
+   "id": "61e0c2d5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -710,7 +710,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f60e93a8",
+   "id": "ca4b6c16",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -738,7 +738,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "949977ea",
+   "id": "e3297b57",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/notebooks/training_regression.ipynb b/notebooks/training_regression.ipynb
index 21d3395..269ce77 100644
--- a/notebooks/training_regression.ipynb
+++ b/notebooks/training_regression.ipynb
@@ -3,19 +3,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "456b62dd",
+   "id": "29b0f025",
    "metadata": {
     "lines_to_next_cell": 2
    },
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "529c71d1",
+   "id": "811f01d9",
    "metadata": {},
    "source": [
     "# Regression with 3D images\n",
@@ -30,7 +30,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5fd3fa64",
+   "id": "23c3bd8f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -65,7 +65,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1c619de7",
+   "id": "7f5449db",
    "metadata": {},
    "source": [
     "\n",
@@ -95,7 +95,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1f70a897",
+   "id": "5840f27e",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -107,7 +107,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29a797aa",
+   "id": "defa27bf",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d13f85d0",
+   "id": "e42d61d4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -129,7 +129,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9466aa23",
+   "id": "86948364",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -140,7 +140,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6f04004f",
+   "id": "5ea2e180",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -151,7 +151,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "92ceff2d",
+   "id": "a35181c9",
    "metadata": {},
    "source": [
     "At the end of this command, a new directory named `deeplearning_prepare_data` is\n",
@@ -162,7 +162,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "107e31e2",
+   "id": "246587b9",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -175,7 +175,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "46c2e69a",
+   "id": "217e7ef0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -184,7 +184,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ca3c0eb7",
+   "id": "3879ace9",
    "metadata": {},
    "source": [
     "ClinicaDL uses the `Conv5_FC3` convolutional network for inputs of type 3D\n",
@@ -199,7 +199,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "167a0a39",
+   "id": "a4faba51",
    "metadata": {},
    "source": [
     "## Before starting \n",
@@ -215,7 +215,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "78444b39",
+   "id": "eb1e7deb",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -230,7 +230,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "691fcb5f",
+   "id": "08b03053",
    "metadata": {},
    "source": [
     "\n",
@@ -257,7 +257,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "581d610f",
+   "id": "c6427c2a",
    "metadata": {},
    "source": [
     "### Prerequisites\n",
@@ -269,7 +269,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "25d9998a",
+   "id": "31deb774",
    "metadata": {},
    "source": [
     "### Running the task\n",
@@ -309,7 +309,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "cb7b0522",
+   "id": "10dce722",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -326,7 +326,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "667c477f",
+   "id": "86fd63c0",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -339,7 +339,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "afc3b850",
+   "id": "b222641d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -350,7 +350,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "38568ee2",
+   "id": "f12ba2ef",
    "metadata": {},
    "source": [
     "The clinicadl train command outputs a MAPS structure in which there are only two data groups: train and validation. \n",
@@ -401,7 +401,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "48386608",
+   "id": "96fd50d4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -415,7 +415,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "45ac7b3d",
+   "id": "fe98a938",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -425,7 +425,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bcf3b494",
+   "id": "6a2bf357",
    "metadata": {},
    "source": [
     "The `predict` functionality performs individual prediction and metrics\n",
@@ -437,7 +437,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d3d58f9a",
+   "id": "c04a6ffb",
    "metadata": {},
    "source": [
     "### Running the task \n",
@@ -463,7 +463,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f18d9a83",
+   "id": "1451b47d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -473,7 +473,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f05009f0",
+   "id": "c44dc188",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -500,7 +500,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b372ae7c",
+   "id": "05675096",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -514,7 +514,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "616e6e46",
+   "id": "dc566247",
    "metadata": {},
    "outputs": [],
    "source": []