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Merge pull request #500 from zivy/updateR
Update the R setup.
2 parents 959533f + 234c9b7 commit 30f30ea

15 files changed

+649
-208
lines changed

‎R/00_Setup.ipynb‎

Lines changed: 28 additions & 8 deletions
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@@ -32,20 +32,32 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"vscode": {
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"languageId": "r"
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}
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},
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"outputs": [],
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"source": [
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"# check that all packages are installed (see requirements.txt file)\n",
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"required_packages <- c(\"SimpleITK\", \"rPython\", \"scatterplot3d\", \"tidyr\", \"ggplot2\", \"xtable\", \"purrr\")\n",
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"required_packages <- c(\"SimpleITK\", \"reticulate\", \"scatterplot3d\", \"tidyr\", \"ggplot2\", \"xtable\", \"purrr\")\n",
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"missing_packages <- required_packages[!unlist(lapply(required_packages, require, character.only = TRUE, quietly = TRUE))]"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"vscode": {
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"languageId": "r"
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}
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},
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"outputs": [],
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"source": [
@@ -67,8 +79,14 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false,
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"simpleitk_error_allowed": "Exception in SITK"
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"simpleitk_error_allowed": "Exception in SITK",
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"vscode": {
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"languageId": "r"
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}
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},
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"outputs": [],
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"source": [
@@ -91,7 +109,9 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true
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"vscode": {
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"languageId": "r"
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}
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},
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"outputs": [],
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"source": [
@@ -111,9 +131,9 @@
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"mimetype": "text/x-r-source",
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"name": "R",
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"pygments_lexer": "r",
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"version": "3.2.3"
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"version": "4.5.1"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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"nbformat_minor": 4
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}

‎R/22_Transforms.ipynb‎

Lines changed: 11 additions & 5 deletions
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@@ -482,7 +482,10 @@
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{
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"cell_type": "markdown",
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"metadata": {
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"collapsed": true
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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}
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},
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"source": [
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"## Similarity to Affine [3D]\n",
@@ -935,7 +938,10 @@
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{
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"cell_type": "markdown",
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"metadata": {
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"collapsed": true
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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}
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},
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"source": [
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"## Writing and Reading\n",
@@ -980,7 +986,7 @@
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"displacement$SetFixedParameters(c(field_size, field_origin, field_spacing, field_direction))\n",
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"displacement$SetParameters(runif(length(displacement$GetParameters())))\n",
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"\n",
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"composite_transform <- Transform(basic_transform)\n",
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"composite_transform <- CompositeTransform(basic_transform)\n",
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"composite_transform$AddTransform(displacement)\n",
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"\n",
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"full_file_name <- file.path(OUTPUT_DIR, \"composite.tfm\")\n",
@@ -1030,9 +1036,9 @@
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"mimetype": "text/x-r-source",
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"name": "R",
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"pygments_lexer": "r",
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"version": "3.5.3"
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"version": "4.5.1"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 1
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"nbformat_minor": 4
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}

‎R/300_Segmentation_Overview.ipynb‎

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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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}
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},
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"outputs": [],
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"source": [
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
@@ -148,7 +154,7 @@
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"seg <- Image(img_T1$GetSize(), \"sitkUInt8\")\n",
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"seg$CopyInformation(img_T1)\n",
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"seg$SetPixel(seed,1)\n",
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"seg <- BinaryDilate(seg, 3)\n",
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"seg <- BinaryDilate(seg, c(3,3,3))\n",
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"\n",
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"Show(LabelOverlay(img_T1_255, seg))"
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]
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"seed <- c(132,142,96)\n",
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"\n",
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"seg <- Image(img_T1$GetSize(), \"sitkUInt8\")\n",
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"seg$CopyInformation(img_T1)\n",
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"seg$SetPixel(seed, 1)\n",
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"seg <- BinaryDilate(seg, 3)"
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"seg <- BinaryDilate(seg, c(3,3,3))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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}
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},
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"outputs": [],
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"source": [
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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}
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},
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"outputs": [],
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"source": [
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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}
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},
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"outputs": [],
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"source": [
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"mimetype": "text/x-r-source",
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"name": "R",
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"pygments_lexer": "r",
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"version": "3.2.3"
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"version": "4.5.1"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 1
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"nbformat_minor": 4
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}

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