Group1

170327-nipype/notebooks/rfmri_group_1/PreprocessingWorkflow.ipynb

@@ -2,23 +2,117 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Import workflow elements\n",
-    "from nipype import Node, Workflow"
+    "from nipype import Node, Workflow\n",
+    "from IPython.display import Image\n",
+    "import warnings\n",
+    "from nipype.interfaces import fsl"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Import necessary interfaces"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# make nodes\n",
+    "node_bet = Node(fsl.BET (functional=True), name='fsl_bet')\n",
+    "# gonna want plots and mat\n",
+    "node_mcFlirt = Node(fsl.MCFLIRT(save_mats=True,save_plots=True), name='motion_corr')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# define workflow\n",
+    "wf = Workflow(name=\"group_workflow\")\n",
+    "wf.base_dir = 'Group_test'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# workflow connect\n",
+    "wf.connect([\n",
+    "    (node_bet, node_mcFlirt, [(\"out_file\", \"in_file\")])\n",
+    "])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "170329-15:02:38,663 workflow INFO:\n",
+      "\t Generated workflow graph: Group_test/group_workflow/graph.dot.png (graph2use=hierarchical, simple_form=True).\n"
+     ]
+    },
+    {
+     "data": {
+      "image/png": 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+      "text/plain": [
+       "<IPython.core.display.Image object>"
+      ]
+     },
+     "execution_count": 22,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "#make neat graph\n",
+    "Image(filename=wf.write_graph())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "170329-15:03:13,141 workflow INFO:\n",
+      "\t Workflow group_workflow settings: ['check', 'execution', 'logging']\n",
+      "170329-15:03:13,194 workflow INFO:\n",
+      "\t Running serially.\n",
+      "170329-15:03:13,199 workflow INFO:\n",
+      "\t Executing node fsl_bet in dir: /home/jovyan/work/170327-nipype/notebooks/rfmri_group_1/Group_test/group_workflow/fsl_bet\n",
+      "170329-15:03:13,261 workflow INFO:\n",
+      "\t Running: bet /home/jovyan/work/ds000114/sub-01/func/sub-01_task-linebisection_bold.nii.gz /home/jovyan/work/170327-nipype/notebooks/rfmri_group_1/Group_test/group_workflow/fsl_bet/sub-01_task-linebisection_bold_brain.nii.gz -F\n"
+     ]
+    }
+   ],
+   "source": [
+    "#define the inputs\n",
+    "wf.inputs.fsl_bet.in_file = '/home/jovyan/work/ds000114/sub-01/func/sub-01_task-linebisection_bold.nii.gz'\n",
+    "execution_graph=wf.run()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

170327-nipype/notebooks/rfmri_group_1/PreprocessingWorkflow.py

@@ -0,0 +1,60 @@
+
+# coding: utf-8
+
+# In[24]:
+
+# Import workflow elements
+from nipype import Node, Workflow
+from IPython.display import Image
+import warnings
+from nipype.interfaces import fsl
+import glob
+
+
+# In[16]:
+
+# Import necessary interfaces
+
+
+# In[17]:
+
+# make nodes
+node_bet = Node(fsl.BET (functional=True), name='fsl_bet')
+# gonna want plots and mat
+node_mcFlirt = Node(fsl.MCFLIRT(save_mats=True,save_plots=True), name='motion_corr')
+
+
+# In[20]:
+
+# define workflow
+wf = Workflow(name="group_workflow")
+#make sure you define a base dir, else it will put everything in the temp dir
+wf.base_dir = 'Group_test'
+
+
+# In[21]:
+
+# workflow connect
+# the out_file is the file produced by bet, which then becomes the input of mcflirt
+wf.connect([
+    (node_bet, node_mcFlirt, [("out_file", "in_file")])
+])
+
+
+# In[22]:
+
+#make neat graph
+Image(filename=wf.write_graph())
+
+
+# In[23]:
+
+#define the inputs
+wf.inputs.fsl_bet.in_file = '/home/jovyan/work/ds000114/sub-01/func/sub-01_task-linebisection_bold.nii.gz'
+execution_graph=wf.run()
+
+
+# In[ ]:
+
+
+