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miykaelmiykael
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FIX: removes the derivative dependencies
1 parent f76a56e commit 7ddb045

5 files changed

+92
-221
lines changed

‎notebooks/basic_iteration.ipynb

Lines changed: 18 additions & 43 deletions
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@@ -18,9 +18,7 @@
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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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"from nipype import Node, Workflow\n",
@@ -42,9 +40,7 @@
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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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"isosmooth = Node(IsotropicSmooth(), name='iso_smooth')"
@@ -60,9 +56,7 @@
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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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"isosmooth.iterables = (\"fwhm\", [4, 8, 16])"
@@ -78,9 +72,7 @@
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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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"# Create the workflow\n",
@@ -104,9 +96,7 @@
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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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"# Visualize the detailed graph\n",
@@ -125,9 +115,7 @@
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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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"!tree /output/smoothflow -I '*txt|*pklz|report*|*.json|*js|*.dot|*.html'"
@@ -143,9 +131,7 @@
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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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"%pylab inline\n",
@@ -182,9 +168,7 @@
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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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"# First, let's specify the list of subjects\n",
@@ -201,9 +185,7 @@
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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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"from nipype import IdentityInterface\n",
@@ -222,15 +204,14 @@
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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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"from os.path import join as opj\n",
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"from nipype.interfaces.io import SelectFiles, DataSink\n",
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"\n",
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"anat_file = opj('derivatives', 'fmriprep', '{subject_id}', 'anat', '{subject_id}_t1w_preproc.nii.gz')\n",
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"anat_file = opj('{subject_id}', 'ses-test', 'anat', '{subject_id}_ses-test_T1w.nii.gz')\n",
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"\n",
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"templates = {'anat': anat_file}\n",
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"\n",
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"selectfiles = Node(SelectFiles(templates,\n",
@@ -258,9 +239,7 @@
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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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"! ls -l /output/datasink/anat_files/"
@@ -285,7 +264,6 @@
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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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"solution2": "hidden",
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"solution2_first": true
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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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"solution2": "hidden"
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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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"solution2": "hidden"
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},
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"outputs": [],
@@ -335,7 +311,6 @@
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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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"solution2": "hidden"
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},
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"outputs": [],
@@ -354,21 +329,21 @@
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python [conda env:cos1]",
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"display_name": "Python 3",
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"language": "python",
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"name": "conda-env-cos1-py"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.12"
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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}
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},
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"nbformat": 4,

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