diff --git a/getting_started/scripts.ipynb b/getting_started/scripts.ipynb
index 7b87ec6388573c9cebb864bdbea98da654593e9c..1d3d705d5b636c281ce97e6a527431c69075847d 100644
--- a/getting_started/scripts.ipynb
+++ b/getting_started/scripts.ipynb
@@ -18,9 +18,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"#!/usr/bin/env python"
@@ -38,9 +36,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"#!/usr/bin/env fslpython"
@@ -60,9 +56,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"import subprocess as sp\n",
@@ -79,9 +73,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"spobj = sp.run(['ls'], stdout = sp.PIPE)"
@@ -97,9 +89,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"spobj = sp.run('ls -la'.split(), stdout = sp.PIPE)\n",
@@ -119,9 +109,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"import os\n",
@@ -143,9 +131,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"commands = \"\"\"\n",
@@ -176,9 +162,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"import sys\n",
@@ -200,19 +184,10 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Usage: bash <input image> <output image>\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
- "%%bash\n",
"#!/bin/bash\n",
"if [ $# -lt 2 ] ; then\n",
" echo \"Usage: $0 <input image> <output image>\"\n",
@@ -238,21 +213,9 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "ename": "IndexError",
- "evalue": "list index out of range",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-2-f7378930c369>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0mspobj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mfsldir\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m'/bin/fslstats'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutfile\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'-V'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstdout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mPIPE\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0msout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mspobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstdout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'utf-8'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 15\u001b[0;31m \u001b[0mvol_vox\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 16\u001b[0m \u001b[0mvol_mm\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Volumes are: '\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvol_vox\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m' in voxels and '\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvol_mm\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m' in mm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;31mIndexError\u001b[0m: list index out of range"
- ],
- "output_type": "error"
- }
- ],
+ "outputs": [],
"source": [
"#!/usr/bin/env fslpython\n",
"import os, sys\n",
@@ -272,55 +235,9 @@
"vol_mm = float(sout.split()[1])\n",
"print('Volumes are: ', vol_vox, ' in voxels and ', vol_mm, ' in mm')"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": []
}
],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.6.2"
- },
- "toc": {
- "colors": {
- "hover_highlight": "#DAA520",
- "running_highlight": "#FF0000",
- "selected_highlight": "#FFD700"
- },
- "moveMenuLeft": true,
- "nav_menu": {
- "height": "105px",
- "width": "252px"
- },
- "navigate_menu": true,
- "number_sections": true,
- "sideBar": true,
- "threshold": 4.0,
- "toc_cell": false,
- "toc_section_display": "block",
- "toc_window_display": false
- }
- },
+ "metadata": {},
"nbformat": 4,
"nbformat_minor": 2
}