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some updates to basic input, input-bids and output after updating dataset; after adding derivatives input requires more updates
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‎notebooks/basic_data_input.ipynb

Lines changed: 55 additions & 47 deletions
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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": null,
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"execution_count": 5,
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"metadata": {
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"collapsed": false,
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"deletable": true,
@@ -91,7 +91,7 @@
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"from nipype import DataGrabber, Node\n",
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"\n",
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"# Create DataGrabber node\n",
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"dg = Node(DataGrabber(infields=['subject_id', 'task_name'],\n",
94+
"dg = Node(DataGrabber(infields=['subject_id', 'ses_name', 'task_name'],\n",
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" outfields=['anat', 'func']),\n",
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" name='datagrabber')\n",
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"\n",
@@ -112,34 +112,35 @@
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"source": [
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"Second, we know that the two files we desire are the the following location:\n",
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"\n",
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" anat = /data/ds000114/sub-01/anat/sub-01_T1w.nii.gz\n",
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" func = /data/ds000114/sub-01/func/sub-01_task-fingerfootlips_bold.nii.gz\n",
115+
" 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\n",
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"\n",
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"We see that the two files only have two dynamic parameters between subjects and task names:\n",
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"We see that the two files only have three dynamic parameters between subjects and task names:\n",
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"\n",
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" subject_id: in this case 'sub-01'\n",
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" task_name: in this case fingerfootlips\n",
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" ses_name: test\n",
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"\n",
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"This means that we can rewrite the paths as follows:\n",
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"\n",
125-
" anat = /data/ds102/[subject_id]/anat/[subject_id]_T1w.nii.gz\n",
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" func = /data/ds102/[subject_id]/func/[subject_id]_task-[task_name]_bold.nii.gz\n",
126+
" anat = /data/ds102/[subject_id]/ses-[ses_name]/anat/sub-[subject_id]_ses-[ses_name]_T1w.nii.gz\n",
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" func = /data/ds102/[subject_id]/ses-[ses_name]/func/sub-[subject_id]_ses-[ses_name]_task-[task_name]_bold.nii.gz\n",
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"\n",
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"Therefore, we need the parameter ``subject_id`` for the anatomical image and the parameter ``subject_id`` and ``task_name`` for the functional image. In the context of DataGabber, this is specified as follows:"
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"Therefore, we need the parameters ``subject_id`` and ``ses_name`` for the anatomical image and the parameters ``subject_id``, ``ses_name`` and ``task_name`` for the functional image. In the context of DataGabber, this is specified as follows:"
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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": 6,
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"metadata": {
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"collapsed": true,
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"deletable": true,
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"editable": true
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},
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"outputs": [],
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"source": [
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"dg.inputs.template_args = {'anat': [['subject_id']],\n",
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" 'func': [['subject_id', 'task_name']]}"
142+
"dg.inputs.template_args = {'anat': [['subject_id', 'ses_name']],\n",
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" 'func': [['subject_id', 'ses_name', 'task_name']]}"
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]
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},
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{
@@ -154,16 +155,16 @@
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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": 7,
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"metadata": {
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"collapsed": true,
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"deletable": true,
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"editable": true
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},
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"outputs": [],
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"source": [
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"dg.inputs.field_template = {'anat': 'sub-%02d/anat/*_T1w.nii.gz',\n",
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" 'func': 'sub-%02d/func/*task-%s_bold.nii.gz'}"
166+
"dg.inputs.field_template = {'anat': 'sub-%02d/ses-%s/anat/*_T1w.nii.gz',\n",
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" 'func': 'sub-%02d/ses-%s/func/*task-%s_bold.nii.gz'}"
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]
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},
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{
@@ -173,7 +174,7 @@
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"editable": true
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},
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"source": [
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"You'll notice that we use ``%s``, ``%02d`` and ``*`` for placeholders in the data paths. ``%s`` is a placeholder for a string and is filled out by ``task_name``. ``%02d`` is a placeholder for a integer number and is filled out by ``subject_id``. ``*`` is used as a wild card, e.g. a placeholder for any possible string combination. This is all to set up the ``DataGrabber`` node."
177+
"You'll notice that we use ``%s``, ``%02d`` and ``*`` for placeholders in the data paths. ``%s`` is a placeholder for a string and is filled out by ``task_name`` or ``ses_name``. ``%02d`` is a placeholder for a integer number and is filled out by ``subject_id``. ``*`` is used as a wild card, e.g. a placeholder for any possible string combination. This is all to set up the ``DataGrabber`` node."
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]
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},
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{
@@ -183,12 +184,12 @@
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"editable": true
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},
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"source": [
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"Now it is up to you how you want to feed the dynamic parameters into the node. You can either do this by using another node (e.g. ``IdentityInterface``) and feed ``subject_id`` and ``task_name`` as connections to the ``DataGrabber`` node or specify them directly as node inputs."
187+
"Now it is up to you how you want to feed the dynamic parameters into the node. You can either do this by using another node (e.g. ``IdentityInterface``) and feed ``subject_id``, ``ses_name`` and ``task_name`` as connections to the ``DataGrabber`` node or specify them directly as node inputs."
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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": 8,
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"metadata": {
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"collapsed": false,
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"deletable": true,
@@ -201,6 +202,7 @@
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"infosource = Node(IdentityInterface(fields=['subject_id', 'task_name']),\n",
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" name=\"infosource\")\n",
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"infosource.inputs.task_name = \"fingerfootlips\"\n",
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"infosource.inputs.ses_name = \"test\"\n",
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"subject_id_list = [1, 2]\n",
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"infosource.iterables = [('subject_id', subject_id_list)]"
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]
@@ -222,12 +224,12 @@
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"editable": true
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},
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"source": [
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"If you specify the inputs to the ``DataGrabber`` node directly, you can do this as follows:"
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"You can also provide the inputs to the ``DataGrabber`` node directly, for one subject you can do this as follows:"
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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": 9,
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"metadata": {
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"collapsed": true,
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"deletable": true,
@@ -237,6 +239,7 @@
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"source": [
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"# Specifying the input fields of DataGrabber directly\n",
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"dg.inputs.subject_id = 1\n",
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"dg.inputs.ses_name = \"test\"\n",
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"dg.inputs.task_name = \"fingerfootlips\""
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]
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},
@@ -252,7 +255,7 @@
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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": false,
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"deletable": true,
@@ -263,19 +266,19 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170716-08:56:43,740 workflow INFO:\n",
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"\t Executing node datagrabber in dir: /tmp/tmplw952u04/datagrabber\n"
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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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]
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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/anat/sub-01_T1w.nii.gz\n",
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"func = /data/ds000114/sub-01/func/sub-01_task-fingerfootlips_bold.nii.gz"
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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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"execution_count": 10,
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"metadata": {},
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"output_type": "execute_result"
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}
@@ -297,20 +300,21 @@
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"\n",
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"Let's focus again on the data we want to import:\n",
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"\n",
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" anat = /data/ds000114/sub-01/anat/sub-01_T1w.nii.gz\n",
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" func = /data/ds000114/sub-01/func/sub-01_task-fingerfootlips_bold.nii.gz\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\n",
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" \n",
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"Now, we can replace those paths with the accoridng {}-based strings.\n",
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"\n",
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" anat = /data/ds000114/sub-{subject_id}/anat/sub-{subject_id}_T1w.nii.gz\n",
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" func = /data/ds000114/sub-{subject_id}/func/sub-{subject_id}_task-{task_name}_bold.nii.gz\n",
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" anat = /data/ds000114/sub-{subject_id}/ses-{ses_name}/anat/sub-{subject_id}_ses-{ses_name}_T1w.nii.gz\n",
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" func = /data/ds000114/sub-{subject_id}/ses-{ses_name}/func/ \\\n",
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" sub-{subject_id}_ses-{ses_name}_task-{task_name}_bold.nii.gz\n",
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"\n",
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"How would this look like as a `SelectFiles` node?"
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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": 12,
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"metadata": {
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"collapsed": false,
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"deletable": true,
@@ -321,8 +325,8 @@
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"from nipype import SelectFiles, Node\n",
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"\n",
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"# String template with {}-based strings\n",
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"templates = {'anat': 'sub-{subject_id}/anat/sub-{subject_id}_T1w.nii.gz',\n",
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" 'func': 'sub-{subject_id}/func/sub-{subject_id}_task-{task_name}_bold.nii.gz'}\n",
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"templates = {'anat': 'sub-{subject_id}/ses-{ses_name}/anat/sub-{subject_id}_ses-{ses_name}_T1w.nii.gz',\n",
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" 'func': 'sub-{subject_id}/ses-{ses_name}/func/sub-{subject_id}_ses-{ses_name}_task-{task_name}_bold.nii.gz'}\n",
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"\n",
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"# Create SelectFiles node\n",
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"sf = Node(SelectFiles(templates),\n",
@@ -333,6 +337,7 @@
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"\n",
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"# Feed {}-based placeholder strings with values\n",
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"sf.inputs.subject_id = '01'\n",
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"sf.inputs.ses_name = \"test\"\n",
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"sf.inputs.task_name = 'fingerfootlips'"
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]
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},
@@ -348,7 +353,7 @@
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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,
@@ -359,19 +364,19 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170716-08:57:26,899 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmpys0agcu4/selectfiles\n"
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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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]
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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/anat/sub-01_T1w.nii.gz\n",
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"func = /data/ds000114/sub-01/func/sub-01_task-fingerfootlips_bold.nii.gz"
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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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"execution_count": 13,
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"metadata": {},
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"output_type": "execute_result"
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}
@@ -398,7 +403,7 @@
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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": 15,
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"metadata": {
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"collapsed": false,
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"deletable": true,
@@ -409,18 +414,18 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170716-08:57:41,262 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmpet7ix46z/selectfiles\n"
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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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]
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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/anat/sub-01_T1w.nii.gz', '/data/ds000114/sub-02/anat/sub-02_T1w.nii.gz']"
425+
"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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"execution_count": 15,
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"metadata": {},
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"output_type": "execute_result"
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}
@@ -430,7 +435,7 @@
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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-0[1,2]/anat/sub-0[1,2]_T1w.nii.gz'}\n",
438+
"templates = {'anat': 'sub-0[1,2]/ses-{ses_name}/anat/sub-0[1,2]_ses-{ses_name}_T1w.nii.gz'}\n",
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"\n",
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"\n",
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"# Create SelectFiles node\n",
@@ -440,6 +445,9 @@
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"# Location of the dataset folder\n",
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"sf.inputs.base_directory = '/data/ds000114'\n",
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"\n",
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"# Feed {}-based placeholder strings with values\n",
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"sf.inputs.ses_name = 'test'\n",
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"\n",
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"# Print SelectFiles output\n",
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"sf.run().outputs"
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]
@@ -453,7 +461,7 @@
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"source": [
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"As you can see, now `anat` contains two file paths, one for the first and one for the second subject. As a side node, you could have also gotten them same thing with the wild card `*`:\n",
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"\n",
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" 'sub-0*/anat/sub-0*_T1w.nii.gz'"
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" 'sub-0*/ses-test/anat/sub-0*_ses-test_T1w.nii.gz'"
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]
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},
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{
@@ -686,9 +694,9 @@
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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": "3.5.2"
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"version": "3.6.2"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 1
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"nbformat_minor": 2
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}

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