From 5cf4ba8bcad54c7bf24609f6cd7a76fb00f3fac1 Mon Sep 17 00:00:00 2001
From: Michael Joseph <josephmje.22@gmail.com>
Date: Thu, 2 Sep 2021 08:21:11 -0400
Subject: [PATCH] fix derivatives

---
 code/05-bids-derivatives.ipynb | 44 ++++------------------------------
 1 file changed, 5 insertions(+), 39 deletions(-)

diff --git a/code/05-bids-derivatives.ipynb b/code/05-bids-derivatives.ipynb
index a27daf3..eb7ca30 100644
--- a/code/05-bids-derivatives.ipynb
+++ b/code/05-bids-derivatives.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "1316c203",
+   "id": "115292ab",
    "metadata": {},
    "source": [
     "## BIDS Apps\n",
@@ -10,44 +10,25 @@
     "[BIDS Apps](https://bids-apps.neuroimaging.io/) are containerized applications that run on BIDS data structures.  \n",
     "\n",
     "Some examples include:\n",
-<<<<<<< HEAD
     "- mriqc\n",
     "- fmriprep\n",
     "- freesurfer\n",
-=======
-    "- freesurfer\n",
-    "- fmriprep (https://fmriprep.readthedocs.io/en/stable/citing.html)\n",
-    "- mriqc\n",
->>>>>>> upstream/gh-pages
     "- ciftify\n",
     "- SPM\n",
     "- MRtrix3_connectome\n",
     "\n",
     "They rely on 2 technologies for container computing:\n",
-<<<<<<< HEAD
     "- <b>Docker</b>\n",
     "  - for building, hosting, and running containers on local hardware (Windows, Mac OS, Linux) or in the cloud\n",
     "- <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": [
+    "<img src=\"../fig/bids_app.png\" alt=\"Drawing\" align=\"middle\" width=\"500px\"/>\n",
+    "\n",
     "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": [
+    "    `singularity build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1`\n",
+    "    \n",
     "To run the container:\n",
     "\n",
     "```\n",
@@ -57,21 +38,6 @@
     "  /data /data/derivatives participant\n",
     "```"
    ]
-=======
-    "- Docker\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"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "e2234bf1",
-   "metadata": {},
-   "outputs": [],
-   "source": []
->>>>>>> upstream/gh-pages
   }
  ],
  "metadata": {