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ME-ICA · Mar 26, 2024 · 68b2c98 · 68b2c98
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diff --git a/_sources/content/00_Download_Data.ipynb b/_sources/content/00_Download_Data.ipynb
diff --git a/_sources/content/01_Optimal_Combination_with_t2smap.ipynb b/_sources/content/01_Optimal_Combination_with_t2smap.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "a972b135",
+   "id": "cdcf0cb2",
    "metadata": {},
    "source": [
     "# Optimal combination with `t2smap`\n",
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "5826ee84",
+   "id": "754699ac",
    "metadata": {},
    "outputs": [
     {
@@ -54,7 +54,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "58f7893a",
+   "id": "57aad9d0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -91,56 +91,56 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "a1524be6",
+   "id": "6a128796",
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO     t2smap:t2smap_workflow:233 Using output directory: /home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/t2smap\n"
+      "INFO     t2smap:t2smap_workflow:238 Using output directory: /home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/t2smap\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO     t2smap:t2smap_workflow:243 Loading input data: ['/home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/func/sub-04570_task-rest_echo-1_space-scanner_desc-partialPreproc_bold.nii.gz', '/home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/func/sub-04570_task-rest_echo-2_space-scanner_desc-partialPreproc_bold.nii.gz', '/home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/func/sub-04570_task-rest_echo-3_space-scanner_desc-partialPreproc_bold.nii.gz', '/home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/func/sub-04570_task-rest_echo-4_space-scanner_desc-partialPreproc_bold.nii.gz']\n"
+      "INFO     t2smap:t2smap_workflow:264 Loading input data: ['/home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/func/sub-04570_task-rest_echo-1_space-scanner_desc-partialPreproc_bold.nii.gz', '/home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/func/sub-04570_task-rest_echo-2_space-scanner_desc-partialPreproc_bold.nii.gz', '/home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/func/sub-04570_task-rest_echo-3_space-scanner_desc-partialPreproc_bold.nii.gz', '/home/runner/work/multi-echo-data-analysis/multi-echo-data-analysis/data/multi-echo-data-analysis/func/sub-04570_task-rest_echo-4_space-scanner_desc-partialPreproc_bold.nii.gz']\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO     t2smap:t2smap_workflow:259 Using user-defined mask\n"
+      "INFO     t2smap:t2smap_workflow:280 Using user-defined mask\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO     t2smap:t2smap_workflow:262 Computing adaptive T2* map\n"
+      "INFO     t2smap:t2smap_workflow:283 Computing adaptive T2* map\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO     t2smap:t2smap_workflow:279 Computing optimal combination\n"
+      "INFO     t2smap:t2smap_workflow:300 Computing optimal combination\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO     combine:make_optcom:191 Optimally combining data with voxel-wise T2* estimates\n"
+      "INFO     combine:make_optcom:192 Optimally combining data with voxel-wise T2* estimates\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO     t2smap:t2smap_workflow:325 Workflow completed\n"
+      "INFO     t2smap:t2smap_workflow:358 Workflow completed\n"
      ]
     }
    ],
@@ -158,7 +158,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "fc2f4ef1",
+   "id": "55f211e7",
    "metadata": {},
    "outputs": [
     {
@@ -184,7 +184,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "id": "fc1c3651",
+   "id": "28415b76",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -202,7 +202,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bbb8d911",
+   "id": "0039d232",
    "metadata": {},
    "source": [
     "```{glue:figure} figure_t2starmap\n",
@@ -216,7 +216,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "f15b06ba",
+   "id": "10cf7b0e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -234,7 +234,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ee80c7b5",
+   "id": "07afcc5c",
    "metadata": {},
    "source": [
     "```{glue:figure} figure_s0map\n",
@@ -248,7 +248,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "id": "340338fc",
+   "id": "995c381b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -307,7 +307,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5a7934bf",
+   "id": "28d2e05e",
    "metadata": {},
    "source": [
     "```{glue:figure} figure_t2smap_epi_plots\n",
@@ -321,7 +321,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "06c90647",
+   "id": "5dc8e336",
    "metadata": {},
    "outputs": [
     {
@@ -385,7 +385,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5df16ad2",
+   "id": "db1d1620",
    "metadata": {},
    "source": [
     "```{glue:figure} figure_t2smap_t2snr\n",
@@ -399,7 +399,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "id": "b8b2287e",
+   "id": "45445223",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -414,7 +414,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "998a7f63",
+   "id": "6332b4f4",
    "metadata": {},
    "source": [
     "```{glue:figure} figure_echo2_carpet\n",
@@ -428,7 +428,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "id": "6f1000cf",
+   "id": "78f86a01",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -442,7 +442,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9300c76e",
+   "id": "c6b8b2a2",
    "metadata": {},
    "source": [
     "```{glue:figure} figure_optcom_carpet\n",