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djareckadjarecka
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Merge pull request djarecka#4 from satra/updates
updated basic notebooks
2 parents 8f2828e + 272ac6d commit 682fc7c

15 files changed

+1461
-1614
lines changed

‎notebooks/basic_configuration.ipynb

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@@ -63,6 +63,9 @@
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"outputs": [],
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"source": [
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"from nipype import config, logging\n",
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"import os\n",
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"os.makedirs('/output/log_folder', exist_ok=True)\n",
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"os.makedirs('/output/crash_folder', exist_ok=True)\n",
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"\n",
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"config_dict={'execution': {'remove_unnecessary_outputs': 'true',\n",
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" 'keep_inputs': 'false',\n",
@@ -71,13 +74,13 @@
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" 'hash_method': 'timestamp',\n",
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" 'local_hash_check': 'true',\n",
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" 'create_report': 'true',\n",
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" 'crashdump_dir': '/opt/tutorial/crash_folder',\n",
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" 'crashdump_dir': '/output/crash_folder',\n",
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" 'use_relative_paths': 'false',\n",
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" 'job_finished_timeout': '5'},\n",
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" 'logging': {'workflow_level': 'INFO',\n",
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" 'filemanip_level': 'INFO',\n",
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" 'interface_level': 'INFO',\n",
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" 'log_directory': '/opt/tutorial/log_folder',\n",
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" 'log_directory': '/output/log_folder',\n",
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" 'log_to_file': 'true'}}\n",
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"config.update_config(config_dict)\n",
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"logging.update_logging(config)"
@@ -114,7 +117,7 @@
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" 'filemanip_level' : 'DEBUG',\n",
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" 'interface_level' : 'DEBUG',\n",
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" 'log_to_file' : 'True',\n",
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" 'log_directory' : '/opt/tutorial/log_folder'}"
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" 'log_directory' : '/output/log_folder'}"
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]
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},
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{

‎notebooks/basic_data_input.ipynb

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@@ -80,7 +80,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 1,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": 2,
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"metadata": {
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"collapsed": true,
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"deletable": true,
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": 3,
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"metadata": {
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"collapsed": true,
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"deletable": true,
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": 4,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": 5,
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"metadata": {
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"collapsed": true,
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"deletable": true,
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"execution_count": 6,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170727-19:13:54,954 workflow INFO:\n",
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"\t Executing node datagrabber in dir: /tmp/tmpzh0nl8du/datagrabber\n"
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"170730-12:25:32,161 workflow INFO:\n",
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"\t Executing node datagrabber in dir: /tmp/tmplmop1pqt/datagrabber\n"
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]
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},
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{
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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": 10,
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"execution_count": 6,
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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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{
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"cell_type": "code",
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"execution_count": 12,
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"execution_count": 7,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"execution_count": 8,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170727-19:18:15,247 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmpkxrlth4a/selectfiles\n"
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"170730-12:25:34,430 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmp5z9bopfl/selectfiles\n"
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]
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},
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{
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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": 13,
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"execution_count": 8,
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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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{
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"cell_type": "code",
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"execution_count": 9,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170727-19:21:09,233 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmphih2czqa/selectfiles\n"
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"170730-12:25:35,400 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmp59333sfs/selectfiles\n"
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]
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},
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{
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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": 15,
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"execution_count": 9,
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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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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 10,
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"metadata": {
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"collapsed": true,
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"deletable": true,
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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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"execution_count": 11,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170716-08:58:08,702 workflow INFO:\n",
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"\t Executing node fssource in dir: /tmp/tmp9rd5qmlb/fssource\n"
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"170730-12:25:39,247 workflow INFO:\n",
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"\t Executing node fssource in dir: /tmp/tmpo_jxbjpx/fssource\n"
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]
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}
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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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"execution_count": 13,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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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']\n",
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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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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"collapsed": false,
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"deletable": true,
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170716-08:58:55,407 workflow INFO:\n",
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"\t Executing node fssource in dir: /tmp/tmp9rd5qmlb/fssource\n"
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"170730-12:25:41,991 workflow INFO:\n",
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"\t Executing node fssource in dir: /tmp/tmpo_jxbjpx/fssource\n"
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]
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}
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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": 15,
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"metadata": {
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"collapsed": false,
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"deletable": true,
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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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"execution_count": 15,
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"metadata": {},
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"output_type": "execute_result"
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}

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