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ENH: changes order of solution and answer cell, plus some other small changes
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‎notebooks/basic_data_input.ipynb

Lines changed: 24 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -236,13 +236,22 @@
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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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"### Exercise 1\n",
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"Grab T1w images from both sessions - ``ses-test`` and ``ses-retest`` for ``sub-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": null,
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"metadata": {
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"solution2": "hidden",
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"solution2_first": true
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},
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"outputs": [],
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"source": [
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"### Exercise 1\n",
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"Grab T1w images from both sessions - ``ses-test`` and ``ses-retest`` for ``sub-01``."
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"# write your solution here"
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]
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},
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{
@@ -291,15 +300,6 @@
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"ex1_res.outputs"
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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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"# write your solution here"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
@@ -383,7 +383,6 @@
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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",
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"\n",
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"# String template with {}-based strings\n",
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"templates = {'anat': 'sub-*/ses-{ses_name}/anat/sub-*_ses-{ses_name}_T1w.nii.gz'}\n",
@@ -416,13 +415,22 @@
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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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"### Exercise 2\n",
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"Use ``SelectFile`` to select again T1w images from both sessions - ``ses-test`` and ``ses-retest`` for ``sub-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": null,
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"metadata": {
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"solution2": "hidden",
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"solution2_first": true
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},
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"outputs": [],
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"source": [
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"### Exercise 2\n",
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"Use ``SelectFile`` to select again T1w images from both sessions - ``ses-test`` and ``ses-retest`` for ``sub-01``."
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"# write your solution here"
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]
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},
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{
@@ -451,15 +459,6 @@
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"sf.run().outputs"
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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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"# write your solution here"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
@@ -482,7 +481,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"!datalad get -r -J4 /data/ds000114/derivatives/freesurfer/sub-01/"
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"!datalad get -r -J4 /data/ds000114/derivatives/freesurfer/sub-01"
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]
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},
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{
@@ -560,7 +559,6 @@
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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",
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"print('inflated: %s\\n' % result.outputs.inflated)"
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]
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},
@@ -608,7 +606,7 @@
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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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},

‎notebooks/basic_data_input_bids.ipynb

Lines changed: 34 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -161,10 +161,7 @@
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"solution2": "hidden",
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"solution2_first": true
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},
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"metadata": {},
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"source": [
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"### Exercise 1:\n",
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"List all files for the \"linebisection\" task for subject 02."
@@ -174,23 +171,26 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden"
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"solution2": "hidden",
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"solution2_first": true
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},
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"outputs": [],
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"source": [
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"from bids.grabbids import BIDSLayout\n",
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"layout = BIDSLayout(\"/data/ds000114/\")\n",
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"\n",
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"[f.filename for f in layout.get(subject='02', task=\"linebisection\")]"
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"#write your solution here"
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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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"metadata": {
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"solution2": "hidden"
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},
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"outputs": [],
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"source": [
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"#write your solution here"
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"from bids.grabbids import BIDSLayout\n",
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"layout = BIDSLayout(\"/data/ds000114/\")\n",
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"\n",
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"[f.filename for f in layout.get(subject='02', task=\"linebisection\")]"
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]
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},
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{
@@ -300,13 +300,22 @@
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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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"### Exercise 2:\n",
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"Modify the `BIDSDataGrabber` and the workflow to collect T1ws images for subject `10`."
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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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"solution2": "hidden",
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"solution2_first": true
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},
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"outputs": [],
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"source": [
308-
"### Exercise 2:\n",
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"Modify the `BIDSDataGrabber` and the workflow to collect T1ws images for subject `10`."
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"# write your solution here"
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]
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},
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{
@@ -340,15 +349,6 @@
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"ex2_res.outputs"
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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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"# write your solution here"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
@@ -421,13 +421,22 @@
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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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"### Exercise 3:\n",
427+
"Modify the `printMetadata` function to also print `EchoTime` "
428+
]
429+
},
430+
{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden",
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"solution2_first": true
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},
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"outputs": [],
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"source": [
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"### Exercise 3:\n",
430-
"Modify the `printMetadata` function to also print `EchoTime` "
439+
"# write your solution here"
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]
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},
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{
@@ -489,20 +498,11 @@
489498
"ex3_wf.connect(ex3_BIDSDataGrabber, \"bolds\", ex3_analyzeBOLD2, \"path\")\n",
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"ex3_wf.run()"
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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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"# write your solution here"
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]
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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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"display_name": "Python [default]",
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"language": "python",
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"name": "python3"
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},

‎notebooks/basic_data_output.ipynb

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -280,13 +280,22 @@
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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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"### Exercise 1\n",
286+
"Create a simple workflow for skullstriping with FSL, the first node should use `BET` interface and the second node will be a ``DataSink``. Test two method of connecting the nodes and check the content of the output directory."
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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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"solution2": "hidden",
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"solution2_first": true
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},
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"outputs": [],
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"source": [
288-
"### Exercise 1\n",
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"Create a simple workflow for skullstriping with FSL, the first node should use `BET` interface and the second node will be a ``DataSink``. Test two method of connecting the nodes and check the content of the output directory."
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"# write your solution here"
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]
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},
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{
@@ -375,21 +384,12 @@
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"# and check the content of the output directory (you should see a new `bet` subdirectory with both files)\n",
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"! tree /output/working_dir/ex1_output"
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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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"# write your solution here"
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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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