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ENH: some stylistic changes
1 parent e8d7cb2 commit 28cfecd

6 files changed

+136
-80
lines changed

‎notebooks/basic_import_workflows.ipynb

Lines changed: 57 additions & 48 deletions
Original file line numberDiff line numberDiff line change
@@ -37,9 +37,7 @@
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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.workflows.fmri.fsl.preprocess import create_susan_smooth\n",
@@ -81,9 +79,7 @@
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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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"!fslmaths /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz \\\n",
@@ -100,9 +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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"smoothwf.inputs.inputnode.in_files = '/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz'\n",
@@ -121,9 +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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"%pylab inline\n",
@@ -142,9 +134,7 @@
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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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"smoothwf.run('MultiProc', plugin_args={'n_procs': 4})"
@@ -160,22 +150,36 @@
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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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"%%bash\n",
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"fslmaths /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz -Tmean fmean.nii.gz\n",
158+
"fslmaths /output/susan_smooth/smooth/mapflow/_smooth0/sub-01_ses-test_task-fingerfootlips_bold_smooth.nii.gz \\\n",
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" -Tmean smean.nii.gz"
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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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"outputs": [],
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"source": [
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"from nilearn import image, plotting"
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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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"outputs": [],
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"source": [
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"!fslmaths /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz -Tmean fmean.nii.gz\n",
169-
"!fslmaths /output/susan_smooth/smooth/mapflow/_smooth0/sub-01_ses-test_task-fingerfootlips_bold_smooth.nii.gz \\\n",
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" -Tmean smean.nii.gz\n",
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"\n",
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"from nilearn import image, plotting\n",
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"plotting.plot_epi(\n",
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" 'fmean.nii.gz', title=\"mean (no smoothing)\", display_mode='z',\n",
175-
" cmap='gray', cut_coords=(-45, -30, -15, 0, 15))\n",
179+
" cmap='gray', cut_coords=(-45, -30, -15, 0, 15));\n",
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"plotting.plot_epi(\n",
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" 'smean.nii.gz', title=\"mean (susan smoothed)\", display_mode='z',\n",
178-
" cmap='gray', cut_coords=(-45, -30, -15, 0, 15))"
182+
" cmap='gray', cut_coords=(-45, -30, -15, 0, 15));"
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]
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},
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{
@@ -190,9 +194,7 @@
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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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"print(smoothwf.list_node_names())"
@@ -208,9 +210,7 @@
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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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"median = smoothwf.get_node('median')"
@@ -226,9 +226,7 @@
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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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"median.inputs.op_string = '-k %s -p 99'"
@@ -244,9 +242,7 @@
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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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"smoothwf.run('MultiProc', plugin_args={'n_procs': 4})"
@@ -262,15 +258,28 @@
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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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"!fslmaths /output/susan_smooth/smooth/mapflow/_smooth0/sub-01_ses-test_task-fingerfootlips_bold_smooth.nii.gz \\\n",
271-
" -Tmean mmean.nii.gz\n",
272-
"\n",
273-
"from nilearn import image, plotting\n",
265+
" -Tmean mmean.nii.gz"
266+
]
267+
},
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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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"outputs": [],
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"source": [
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"from nilearn import image, plotting"
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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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"outputs": [],
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"source": [
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"plotting.plot_epi(\n",
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" 'smean.nii.gz', title=\"mean (susan smooth)\", display_mode='z',\n",
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" cmap='gray', cut_coords=(-45, -30, -15, 0, 15))\n",
@@ -283,21 +292,21 @@
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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 [default]",
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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",
299-
"pygments_lexer": "ipython2",
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"version": "2.7.12"
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"pygments_lexer": "ipython3",
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

‎notebooks/basic_interfaces_caching.ipynb

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -80,7 +80,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"! ls -l /output/workingdir_mem/nipype_mem"
83+
"! ls -lh /output/workingdir_mem/nipype_mem"
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]
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},
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{
@@ -148,7 +148,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python [default]",
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"language": "python",
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"name": "python3"
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},

‎notebooks/basic_iteration.ipynb

Lines changed: 51 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -134,23 +134,63 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"%pylab inline\n",
138-
"from nilearn import plotting\n",
137+
"%matplotlib inline\n",
138+
"from nilearn import plotting"
139+
]
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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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"outputs": [],
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"source": [
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"plotting.plot_anat(\n",
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" '/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz', title='original',\n",
141-
" display_mode='z', cut_coords=(-50, -35, -20, -5), annotate=False)\n",
149+
" display_mode='z', dim=-1, cut_coords=(-50, -35, -20, -5), annotate=False);"
150+
]
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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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"outputs": [],
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"source": [
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"plotting.plot_anat(\n",
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" '/output/smoothflow/skullstrip/sub-01_ses-test_T1w_brain.nii.gz', title='skullstripped',\n",
144-
" display_mode='z', cut_coords=(-50, -35, -20, -5), annotate=False)\n",
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" display_mode='z', dim=-1, cut_coords=(-50, -35, -20, -5), annotate=False);"
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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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"outputs": [],
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"source": [
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"plotting.plot_anat(\n",
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" '/output/smoothflow/_fwhm_4/iso_smooth/sub-01_ses-test_T1w_brain_smooth.nii.gz', title='FWHM=4',\n",
147-
" display_mode='z', cut_coords=(-50, -35, -20, -5), annotate=False)\n",
171+
" display_mode='z', dim=-0.5, cut_coords=(-50, -35, -20, -5), annotate=False);"
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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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"outputs": [],
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"source": [
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"plotting.plot_anat(\n",
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" '/output/smoothflow/_fwhm_8/iso_smooth/sub-01_ses-test_T1w_brain_smooth.nii.gz', title='FWHM=8',\n",
150-
" display_mode='z', cut_coords=(-50, -35, -20, -5), annotate=False)\n",
182+
" display_mode='z', dim=-0.5, cut_coords=(-50, -35, -20, -5), annotate=False);"
183+
]
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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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"outputs": [],
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"source": [
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"plotting.plot_anat(\n",
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" '/output/smoothflow/_fwhm_16/iso_smooth/sub-01_ses-test_T1w_brain_smooth.nii.gz', title='FWHM=16',\n",
153-
" display_mode='z', cut_coords=(-50, -35, -20, -5), annotate=False)"
193+
" display_mode='z', dim=-0.5, cut_coords=(-50, -35, -20, -5), annotate=False);"
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]
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},
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{
@@ -242,7 +282,7 @@
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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/"
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"! ls -lh /output/datasink/anat_files/"
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]
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},
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{
@@ -256,7 +296,7 @@
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"#### Exercise 1\n",
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"## Exercise 1\n",
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"Create a workflow to calculate a various powers of ``2`` using two nodes, one for ``IdentityInterface`` with ``iterables``, and one for ``Function`` interface to calculate power of ``2``."
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]
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},
@@ -329,7 +369,7 @@
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python [default]",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

‎notebooks/example_2ndlevel.ipynb

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@@ -241,9 +241,7 @@
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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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"scrolled": true
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"l2analysis.run('MultiProc', plugin_args={'n_procs': 4})"
@@ -495,24 +493,24 @@
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"source": [
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"from nilearn.plotting import plot_glass_brain\n",
497495
"plot_glass_brain(\n",
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" '/output/datasink/2ndLevel/spm_con_0005_fwhm4/spmT_0001_thr.nii',\n",
496+
" '/output/datasink/2ndLevel/spm_con_0005_fwhm4/spmT_0001_thr.nii', colorbar=True,\n",
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" threshold=2, display_mode='lyrz', black_bg=True, vmax=10, title='spm_fwhm4');\n",
500498
"plot_glass_brain(\n",
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" '/output/datasink/2ndLevel/ants_con_0005_fwhm4/spmT_0001_thr.nii',\n",
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" '/output/datasink/2ndLevel/ants_con_0005_fwhm4/spmT_0001_thr.nii', colorbar=True,\n",
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" threshold=2, display_mode='lyrz', black_bg=True, vmax=10, title='ants_fwhm4');\n",
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"plot_glass_brain(\n",
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" '/output/datasink/2ndLevel/spm_con_0005_fwhm8/spmT_0001_thr.nii',\n",
502+
" '/output/datasink/2ndLevel/spm_con_0005_fwhm8/spmT_0001_thr.nii', colorbar=True,\n",
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" threshold=2, display_mode='lyrz', black_bg=True, vmax=10, title='spm_fwhm8');\n",
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"plot_glass_brain(\n",
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" '/output/datasink/2ndLevel/ants_con_0005_fwhm8/spmT_0001_thr.nii',\n",
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" '/output/datasink/2ndLevel/ants_con_0005_fwhm8/spmT_0001_thr.nii', colorbar=True,\n",
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" threshold=2, display_mode='lyrz', black_bg=True, vmax=10, title='ants_fwhm8');"
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]
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}
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],
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python [default]",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

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