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clear outputs
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notebooks/basic_data_input.ipynb

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@@ -229,28 +229,7 @@
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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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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:02:02,387 workflow INFO:\n",
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"\t Executing node datagrabber in dir: /tmp/tmpiwew6ysu/datagrabber\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"\n",
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"anat = /data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\n",
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"func = /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz"
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]
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},
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"execution_count": null,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"outputs": [],
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"source": [
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"dg.run().outputs"
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]
@@ -313,28 +292,7 @@
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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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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:02:02,435 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmpd3odxyze/selectfiles\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"\n",
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"anat = /data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\n",
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"func = /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz"
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]
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},
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"execution_count": null,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"outputs": [],
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"source": [
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"sf.run().outputs"
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]
@@ -356,27 +314,7 @@
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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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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:02:02,458 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmp53bxb6rj/selectfiles\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"\n",
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"anat = ['/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz', '/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz']"
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]
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},
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"execution_count": null,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"outputs": [],
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"source": [
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"from nipype import SelectFiles, Node\n",
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"from os.path import abspath as opap\n",
@@ -488,16 +426,7 @@
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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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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:04:52,28 workflow INFO:\n",
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"\t Executing node fssource in dir: /tmp/tmpisu77m7r/fssource\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"fssource.inputs.subject_id = 'sub-01'\n",
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"result = fssource.run() "
@@ -514,20 +443,7 @@
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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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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"aparc_aseg: ['/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc+aseg.mgz', '/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc.a2009s+aseg.mgz', '/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc.dktatlas+aseg.mgz']\n",
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"\n",
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"brainmask: /data/ds000114/derivatives/freesurfer/sub-01/mri/brainmask.mgz\n",
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"\n",
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"inflated: ['/data/ds000114/derivatives/freesurfer/sub-01/surf/rh.inflated', '/data/ds000114/derivatives/freesurfer/sub-01/surf/lh.inflated']\n",
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"\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"print('aparc_aseg: %s\\n' % result.outputs.aparc_aseg)\n",
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"print('brainmask: %s\\n' % result.outputs.brainmask)\n",
@@ -545,16 +461,7 @@
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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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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:04:54,346 workflow INFO:\n",
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"\t Executing node fssource in dir: /tmp/tmpisu77m7r/fssource\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"fssource.inputs.hemi = 'lh'\n",
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"result = fssource.run()"
@@ -571,18 +478,7 @@
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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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{
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"data": {
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"text/plain": [
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"'/data/ds000114/derivatives/freesurfer/sub-01/surf/lh.inflated'"
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]
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},
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"execution_count": null,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"outputs": [],
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"source": [
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"result.outputs.inflated"
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]

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