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adding notebooks from Satra hands-on
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‎notebooks/bids.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Failed to import duecredit due to No module named 'duecredit'\n"
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]
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}
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],
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"source": [
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"import bids"
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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": 2,
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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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"<module 'bids' from '/opt/miniconda-latest/lib/python3.6/site-packages/bids/__init__.py'>"
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]
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},
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"execution_count": 2,
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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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"source": [
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"bids\n"
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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": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"layout = bids.BIDSLayout(\"ds000003\")"
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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": 4,
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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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"BIDS Layout: .../data/ds000003 | Subjects: 13 | Sessions: 0 | Runs: 0"
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]
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},
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"execution_count": 4,
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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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"source": [
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"layout\n"
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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": 5,
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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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"[<BIDSFile filename='.git/annex/objects/29/WX/MD5E-s25362403--d72afc284b7608e29ab1e92c75513f69.nii.gz/MD5E-s25362403--d72afc284b7608e29ab1e92c75513f69.nii.gz'>,\n",
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" <BIDSFile filename='.git/annex/objects/J3/q7/MD5E-s664614--0f8bc47f9c3047b340abfcd3ce1fb021.nii.gz/MD5E-s664614--0f8bc47f9c3047b340abfcd3ce1fb021.nii.gz'>,\n",
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" <BIDSFile filename='.git/annex/objects/jJ/2v/MD5E-s5712417--0d1e0a7ff7063250404f45a955a66203.nii.gz/MD5E-s5712417--0d1e0a7ff7063250404f45a955a66203.nii.gz'>,\n",
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" <BIDSFile filename='CHANGES'>,\n",
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" <BIDSFile filename='dataset_description.json'>,\n",
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" <BIDSFile filename='participants.tsv'>,\n",
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" <BIDSFile filename='README'>,\n",
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" <BIDSFile filename='sub-01/anat/sub-01_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-01/anat/sub-01_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-01/func/sub-01_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-01/func/sub-01_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-02/anat/sub-02_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-02/anat/sub-02_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-02/func/sub-02_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-02/func/sub-02_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-03/anat/sub-03_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-03/anat/sub-03_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-03/func/sub-03_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-03/func/sub-03_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-04/anat/sub-04_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-04/anat/sub-04_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-04/func/sub-04_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-04/func/sub-04_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-05/anat/sub-05_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-05/anat/sub-05_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-05/func/sub-05_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-05/func/sub-05_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-06/anat/sub-06_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-06/anat/sub-06_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-06/func/sub-06_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-06/func/sub-06_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-07/anat/sub-07_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-07/anat/sub-07_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-07/func/sub-07_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-07/func/sub-07_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-08/anat/sub-08_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-08/anat/sub-08_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-08/func/sub-08_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-08/func/sub-08_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-09/anat/sub-09_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-09/anat/sub-09_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-09/func/sub-09_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-09/func/sub-09_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-10/anat/sub-10_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-10/anat/sub-10_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-10/func/sub-10_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-10/func/sub-10_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-11/anat/sub-11_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-11/anat/sub-11_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-11/func/sub-11_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-11/func/sub-11_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-12/anat/sub-12_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-12/anat/sub-12_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-12/func/sub-12_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-12/func/sub-12_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='sub-13/anat/sub-13_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-13/anat/sub-13_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-13/func/sub-13_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-13/func/sub-13_task-rhymejudgment_events.tsv'>,\n",
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" <BIDSFile filename='task-rhymejudgment_bold.json'>]"
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]
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},
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"execution_count": 5,
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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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"source": [
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"layout.get()"
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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": 6,
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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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"OrderedDict([('bids.subject', <grabbit.core.Entity at 0x7fb7ec35a588>),\n",
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" ('bids.session', <grabbit.core.Entity at 0x7fb7ec35aa20>),\n",
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" ('bids.task', <grabbit.core.Entity at 0x7fb7ec35aa58>),\n",
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" ('bids.acquisition', <grabbit.core.Entity at 0x7fb7ec35ad30>),\n",
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" ('bids.ce', <grabbit.core.Entity at 0x7fb7ec35a9e8>),\n",
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" ('bids.reconstruction', <grabbit.core.Entity at 0x7fb7ec35a518>),\n",
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" ('bids.dir', <grabbit.core.Entity at 0x7fb7ec35aa90>),\n",
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" ('bids.run', <grabbit.core.Entity at 0x7fb7ec35ab38>),\n",
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" ('bids.proc', <grabbit.core.Entity at 0x7fb7ec35ac50>),\n",
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" ('bids.modality', <grabbit.core.Entity at 0x7fb7ec35abe0>),\n",
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" ('bids.echo', <grabbit.core.Entity at 0x7fb7ec35acc0>),\n",
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" ('bids.recording', <grabbit.core.Entity at 0x7fb7ec35ae80>),\n",
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" ('bids.suffix', <grabbit.core.Entity at 0x7fb7ec35ac88>),\n",
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" ('bids.scans', <grabbit.core.Entity at 0x7fb7ec35ad68>),\n",
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" ('bids.fmap', <grabbit.core.Entity at 0x7fb7ec35add8>),\n",
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" ('bids.datatype', <grabbit.core.Entity at 0x7fb7ec35acf8>)])"
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]
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},
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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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"source": [
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"layout.entities"
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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": 7,
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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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"[<BIDSFile filename='sub-01/anat/sub-01_inplaneT2.nii.gz'>,\n",
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" <BIDSFile filename='sub-01/anat/sub-01_T1w.nii.gz'>,\n",
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" <BIDSFile filename='sub-01/func/sub-01_task-rhymejudgment_bold.nii.gz'>,\n",
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" <BIDSFile filename='sub-01/func/sub-01_task-rhymejudgment_events.tsv'>]"
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]
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},
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"execution_count": 7,
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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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"source": [
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"layout.get(subject=\"01\")"
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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": 8,
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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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"['06', '05', '04', '07', '10', '12', '03', '13', '02', '09', '11', '08', '01']"
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]
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},
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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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"source": [
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"layout.get_subjects()"
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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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"outputs": [],
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"source": [
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"from nipype.interfaces.fsl import BET"
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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": 10,
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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/ds000003/sub-01/anat/sub-01_T1w.nii.gz'"
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]
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},
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"execution_count": 10,
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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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"source": [
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"layout.get(subject=\"01\", suffix=\"T1w\", return_type=\"file\")[0]"
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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": 13,
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"metadata": {},
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"outputs": [],
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"source": [
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"res=BET(in_file=layout.get(subject=\"01\", suffix=\"T1w\", return_type=\"file\")[0], out_file=\"brain.nii.gz\").run()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"writting a simple workflow to the script"
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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": 16,
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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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"Overwriting myscripy.py\n"
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]
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}
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],
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"source": [
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"%%writefile myscripy.py\n",
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"\n",
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"import bids\n",
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"from nipype.interfaces.fsl import BET\n",
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"\n",
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"layout = bids.BIDSLayout(\"/data/ds000003\")\n",
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"res=BET(in_file=layout.get(subject=\"01\", suffix=\"T1w\", return_type=\"file\")[0], out_file=\"brain.nii.gz\").run()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## in the jupyter terminal"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"```\n",
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"ls /data/ds000003\n",
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"mkdir scripts\n",
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"cp /data/myscripy.py /data/ds000003/scripts\n",
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"git add scripts/myscripy.py\n",
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"git commit -am \"adding the script\"\n",
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"datalad run python scripts/myscripy.py\n",
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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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"metadata": {},
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"outputs": [],
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"source": []
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}
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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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"language": "python",
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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": 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": "ipython3",
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"version": "3.6.7"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

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