Merge pull request #27 from josephmje/gh-pages

ENH: Update bids

binder/postBuild

@@ -10,9 +10,9 @@ gzip -d data/dicom_examples/0219191_mystudy-0219-1114/dcm/*dcm.gz
 rm data/0219191_mystudy-0219-1114.tar.gz
 
 # Convert DICOM to NIfTI
-mkdir -p data/dicom_examples/nii
-dcm2niix -z y -o data/dicom_examples/nii data/dicom_examples/0219191_mystudy-0219-1114/dcm
-rm -fr data/dicom_examples/nii/*scout*
+mkdir -p data/dicom_examples/0219191_mystudy-0219-1114/nii
+dcm2niix -z y -o data/dicom_examples/0219191_mystudy-0219-1114/nii data/dicom_examples/0219191_mystudy-0219-1114/dcm
+rm -fr data/dicom_examples/0219191_mystudy-0219-1114/nii/*scout*
 
 # Set up git
 git config --global --add user.name "Carl Jacobi"

code/03-brain-imaging-data-structure.ipynb

@@ -193,10 +193,7 @@
    "source": [
     "%%bash\n",
     "\n",
-    "cd ../data/dicom_examples/0219191_mystudy-0219-1114\n",
-    "mkdir dcm2bids\n",
-    "\n",
-    "dcm2bids_scaffold dcm2bids/"
+    "dcm2bids_scaffold -o ../data/dicom_examples/0219191_mystudy-0219-1114/dcm2bids/"
    ]
   },
   {
@@ -207,7 +204,9 @@
    "source": [
     "%%bash\n",
     "\n",
-    "dcm2bids_helper -d ../data/dicom_examples/0219191_mystudy-0219-1114"
+    "dcm2bids_helper \\\n",
+    "  -d ../data/dicom_examples/0219191_mystudy-0219-1114/dcm \\\n",
+    "  -o ../data/dicom_examples/0219191_mystudy-0219-1114/dcm2bids"
    ]
   },
   {
@@ -218,7 +217,12 @@
    "source": [
     "%%bash\n",
     "\n",
-    "dcm2bids -d 0219191_mystudy-0219-1114/ -p 01 -s 01 -c code/config.json -o dcm2bids/"
+    "mkdir -p ../data/dicom_examples/0219191_mystudy-0219-1114/dcm2bids/rawdata\n",
+    "dcm2bids \\\n",
+    "  -d ../data/dicom_examples/0219191_mystudy-0219-1114/dcm \\\n",
+    "  -p 01 -s 01 \\\n",
+    "  -c ../data/dicom_examples/0219191_mystudy-0219-1114/dcm2bids/code/config.json \\\n",
+    "  -o ../data/dicom_examples/0219191_mystudy-0219-1114/dcm2bids/rawdata"
    ]
   },
   {

code/05-bids-derivatives.ipynb

@@ -10,27 +10,51 @@
     "[BIDS Apps](https://bids-apps.neuroimaging.io/) are containerized applications that run on BIDS data structures.  \n",
     "\n",
     "Some examples include:\n",
-    "- freesurfer\n",
-    "- fmriprep (https://fmriprep.readthedocs.io/en/stable/citing.html)\n",
     "- mriqc\n",
+    "- fmriprep\n",
+    "- freesurfer\n",
     "- ciftify\n",
     "- SPM\n",
     "- MRtrix3_connectome\n",
     "\n",
     "They rely on 2 technologies for container computing:\n",
-    "- Docker\n",
+    "- <b>Docker</b>\n",
     "  - for building, hosting, and running containers on local hardware (Windows, Mac OS, Linux) or in the cloud\n",
-    "- Singularity\n",
-    "  - for running containers on high performance compute clusters"
+    "- <b>Singularity</b>\n",
+    "  - for running containers on high performance compute clusters\n",
+    "  \n",
+    "<img src=\"../fig/bids_app.png\" alt=\"Drawing\" align=\"middle\" width=\"500px\"/>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "026bb764",
+   "metadata": {},
+   "source": [
+    "Building a singularity container is as easy as:\n",
+    "    \n",
+    "    `singularity build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1`"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "65420f23",
+   "metadata": {},
+   "source": [
+    "To run the container:\n",
+    "\n",
+    "```\n",
+    "singularity run --cleanenv \\\n",
+    "  -B bids_folder:/data \\\n",
+    "  mriqc-0.16.1.simg \\\n",
+    "  /data /data/derivatives participant\n",
+    "```"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "e2234bf1",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {