Update to latest version

.circleci/config.yml

@@ -8,7 +8,7 @@ jobs:
     steps:
       - checkout
       - run:
-          name: Set up environment
+          name: Run tests
           command: |
             conda create -n py36_env python=3.6 numpy pytest matplotlib -yq
             source activate py36_env

.github/workflows/jekyll.yml

@@ -0,0 +1,20 @@
+name: Jekyll site CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Build the site in the jekyll/builder container
+      run: |
+        docker run \
+        -v ${{ github.workspace }}:/srv/jekyll -v ${{ github.workspace }}/_site:/srv/jekyll/_site \
+        jekyll/builder:latest /bin/bash -c "chmod 777 /srv/jekyll && jekyll build --future"

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "[html]": {
+        "editor.tabSize": 4
+    }
+}

_includes/functions/get_drive_url.html

@@ -1,4 +1,9 @@
-{% assign temp = include.url | split: 'open?id=' %}
-{% assign temp2 = temp[1] %}
-{% assign out_url = 'https://drive.google.com/uc?export=&confirm=no_antivirus&id='| append: temp2 %}
+{% assign url = include.url %}
+{% if url contains 'open?id=' %}
+    {% assign temp = url | split: 'open?id=' %}
+    {% assign temp2 = temp[1] %}
+    {% assign out_url = 'https://drive.google.com/uc?export=&confirm=no_antivirus&id='| append: temp2 %}
+{% else %}
+    {% assign out_url = url %}
+{% endif %}
 {{ out_url }}

_includes/themes/lab/member.html

@@ -12,7 +12,7 @@
 <div class="row">
 	<div class="col-md-3">
 		<div class="media">
-			<img class="pull-left pad-right big-member-photo" src="{{ image }}" style="width:250px; height:auto; padding:1px; border:1px solid #021a40;">
+			<img class="pull-left pad-right big-member-photo" src="{{ image }}">
 		</div>
 		<div class="bigspacer"></div>
 
@@ -48,10 +48,23 @@
 			<div class="bigspacer"></div>
 		{% endif %}
 
+		{% if member.nih_biosketch %}
+			<div class="smallhead">
+				<i class="fa fa-paragraph fa-fw"></i>
+				{% capture biosketch_url %}
+					{% include /functions/get_drive_url.html url=member.nih_biosketch %}
+				{% endcapture %}
+				<a class="social nih_biosketch" href="{{ biosketch_url }}">
+					NIH Biosketch
+				</a>
+			</div>
+			<div class="bigspacer"></div>
+		{% endif %}
+
 		{% if member.orcid %}
 			<div class="smallhead">
 				<i class="ai ai-orcid"></i>
-				<a class="social orcid" href="https://orcid.org/{{ member.orcid }}">
+				<a class="social orcid" href="https://orcid.org/{{ member.orcid }}" title="ORCID">
 					{{ member.orcid }}
 				</a>
 			</div>
@@ -61,7 +74,7 @@
 		{% if member.github %}
 			<div class="smallhead">
 				<i class="fa fa-github-alt fa-fw"></i>
-				<a class="social github" href="https://github.com/{{ member.github }}">
+				<a class="social github" href="https://github.com/{{ member.github }}" title="GitHub">
 					{{ member.github }}
 				</a>
 			</div>
@@ -71,7 +84,7 @@
 		{% if member.twitter %}
 			<div class="smallhead">
 				<i class="fa fa-twitter fa-fw"></i>
-				<a class="social twitter" href="https://twitter.com/{{ member.twitter }}">
+				<a class="social twitter" href="https://twitter.com/{{ member.twitter }}" title="Twitter">
 					@{{ member.twitter }}
 				</a>
 			</div>
@@ -203,8 +216,10 @@
 				{% for project in site.categories.projects %}
 					{% if project.contributors contains member.handle %}
 						  <div class="pad-left note"><p>
-							{% if project.tags contains "software" %}
-								<a href="{{ project.url }}" class="off">[SOFTWARE] {{ project.title }}</a>
+							{% if project.type == "software" %}
+                                <a href="{{ project.url }}" class="off">[SOFTWARE] {{ project.title }}</a>
+                            {% elsif project.type == "pilot" %}
+                                <a href="{{ project.url }}" class="off">[PILOT] {{ project.title }}</a>
 							{% else %}
 								<a href="{{ project.url }}" class="off">{{ project.title }}</a>
 							{% endif %}

assets/themes/lab/css/style.scss

@@ -65,6 +65,10 @@ a.cv:hover {
 	color:#00A08A;
 }
 
+a.nih_biosketch:hover {
+	color:#0fb000;
+}
+
 a.github:hover {
   color: #F2AD00;
 }
@@ -169,14 +173,18 @@ a.off {
 }
 
 .big-member-photo {
-	height: 400px;
-	width: 267;
-	// max-width: 300px;
+    border-radius: 50%;
+    width: 250px;
+    height:auto;
+    padding:1px;
+    border:1px solid #021a40;
 }
 
 .member-photo {
-	height: 150px;
-	width: 100px;
+    width: 175px;
+    height:175px;
+    border:1px solid #021a40;
+    border-radius: 50%;
 }
 
 .member-name {

grab_articles.ipynb

@@ -63,8 +63,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Total number of publications containing \"Laird AR\"[AUTH] AND (\"2012/01/01\"[PDAT] : \"3000/12/31\"[PDAT]): 114\n",
-      "Total number of publications containing \"Sutherland MT\"[AUTH] AND (\"2012/01/01\"[PDAT] : \"3000/12/31\"[PDAT]): 37\n"
+      "Total number of publications containing \"Laird AR\"[AUTH] AND (\"2012/01/01\"[PDAT] : \"3000/12/31\"[PDAT]): 115\n",
+      "Total number of publications containing \"Sutherland MT\"[AUTH] AND (\"2012/01/01\"[PDAT] : \"3000/12/31\"[PDAT]): 39\n"
      ]
     }
    ],
@@ -144,8 +144,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "133 articles found.\n",
-      "127 articles with PubMed IDs found.\n"
+      "137 articles found.\n",
+      "130 articles with PubMed IDs found.\n"
      ]
     }
    ],
@@ -194,7 +194,7 @@
       " 'sleep med rev' 'front ict' 'nat hum behav' 'exp clin psychopharmacol'\n",
       " 'sci adv' 'npj sci learn' 'front neurol' 'drug alcohol depend'\n",
       " 'biol psychiatry cogn neurosci neuroimaging' 'nature' 'am j psychiatry'\n",
-      " 'res synth methods']\n"
+      " 'res synth methods' 'dev psychobiol' 'j adolesc health']\n"
      ]
     }
    ],
@@ -208,15 +208,7 @@
    "cell_type": "code",
    "execution_count": 7,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "New file created for 33075692\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Create files for new articles\n",
     "for _, row in df.iterrows():\n",
@@ -252,9 +244,9 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [conda env:python3]",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "conda-env-python3-py"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -266,7 +258,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

misc/_posts/2015-04-22-home.md

@@ -5,4 +5,12 @@ categories:
  - home
 homepage: true
 ---
-The Neuroinformatics and Brain Connectivity (NBC) Laboratory focuses on characterizing activation within and between brain regions among healthy individuals and those diagnosed with neuropsychiatric disorders. With emphasis on development of data analysis algorithms, neuroscience informatics tools, and neuroimaging ontologies, the Lab’s mission is to enhance understanding of (dys)functional brain networks in health and disease. Improved understanding of such brain networks may impact educational trajectories for students (e.g., the [Adolescent Brain Cognitive Development (ABCD) Study](/projects/abcd)), as well as treatment outcomes for patients (e.g., [Impact of HIV and Cannabis on Brain Function](/projects/hiv-cannabis)). Through our various projects, the Lab aims to address real-world issues. If you would like to know more about specific projects, you are welcome to visit us on [GitHub](https://github.com/NBCLab) and the [Open Science Framework](https://osf.io/m4x75/).
+The Neuroinformatics and Brain Connectivity (NBC) Laboratory is a cognitive neuroimaging research lab based at [Florida International University](https://www.fiu.edu) in Miami, Florida, led by Drs. [Angela Laird](https://nbclab.github.io/team/laird-angela) and [Matthew Sutherland](https://nbclab.github.io/team/sutherland-matthew).
+
+The NBC Lab is located on FIU’s [MMC Campus](https://campusmaps.fiu.edu/docs/MMC.pdf) in the [Academic Health Center 4](https://campusmaps.fiu.edu/index.html#/campus/MMC) building (AHC-4 Room 380).
+
+The NBC Lab uses functional magnetic resonance imaging (fMRI), combined with functional connectivity, meta-analysis, and neuroinformatics approaches, to study the functional organization of the human brain.
+
+Our work focuses on understanding brain function in the context of substance use, adolescent development, and educational learning. To achieve these goals, we embrace open science principles and adopt best practices to promote reproducible neuroimaging results. If you would like to know more about specific projects, you are welcome to visit us on [GitHub](https://github.com/NBCLab) and the [Open Science Framework](https://osf.io/m4x75/). For more about the NBC Lab, please see our [Lab Handbook](https://docs.google.com/document/d/12QHTfVnjxmVAk9pki2hhspnFJB7QeDR3scstHV8KE_c/edit?usp=sharing).
+
+Miami is a vibrant, multicultural, and multilingual urban metropolis. Collectively, the NBC Lab seeks to foster a welcoming and inclusive environment that provides opportunities to support a diverse group of trainees, while engaging with participant groups who have been historically underrepresented in research, including communities of color.

papers/_posts/2018-01-01-yanes-neuroimaging-meta-analysis-of.md

@@ -10,7 +10,7 @@ issue: 3
 pages: 283-295
 is_published: true
 image: /assets/images/papers/j-psychopharmacol.png
-projects: []
+projects: ["pace"]
 tags: [meta-analysis]
 
 # Text

papers/_posts/2018-01-09-muller-ten-simple-rules.md

@@ -10,7 +10,7 @@ issue:
 pages: 151-161
 is_published: true
 image: /assets/images/papers/neurosci-biobehav-rev.png
-projects: []
+projects: ["pace", "athena"]
 tags: []
 
 # Text

papers/_posts/2018-02-01-sutherland-functional-neurocircuits-and.md

@@ -10,7 +10,7 @@ issue: 2
 pages: 129-143
 is_published: true
 image: /assets/images/papers/trends-mol-med.png
-projects: []
+projects: ["pace"]
 tags: []
 
 # Text

papers/_posts/2018-02-26-riedel-dissociable-meta-analytic-brain.md

@@ -10,7 +10,7 @@ issue:
 pages:
 is_published: true
 image: /assets/images/papers/hum-brain-mapp.png
-projects: []
+projects: ["pace", "athena"]
 tags: [meta-analysis]
 
 # Text

papers/_posts/2019-03-02-bottenhorn-cooperating-yet-distinct.md

@@ -10,7 +10,7 @@ issue: 1
 pages: 27-48
 is_published: true
 image: /assets/images/papers/netw-neurosci.png
-projects:
+projects: ["pace", "athena"]
 tags: [preprint, meta-analysis]
 
 # Text

papers/_posts/2019-05-23-yanes-effects-of-cannabinoid.md

@@ -10,7 +10,7 @@ issue:
 pages:
 is_published: true
 image: /assets/images/papers/exp-clin-psychopharmacol.png
-projects:
+projects: ["pace"]
 tags: []
 
 # Text

papers/_posts/2019-10-22-flannery-habenular-and-striatal.md

@@ -10,7 +10,7 @@ issue: 10
 pages: eaax2084
 is_published: true
 image: /assets/images/papers/sci-adv.png
-projects:
+projects: ["pace"]
 tags: [preprint]
 
 # Text

papers/_posts/2019-12-23-flannery-metaanalytic-clustering-dissociates.md

@@ -10,7 +10,7 @@ issue:
 pages:
 is_published: true
 image: /assets/images/papers/cogn-affect-behav-neurosci.png
-projects:
+projects: ["pace", "athena"]
 tags: [preprint]
 
 # Text

papers/_posts/2020-01-22-waller-disruptive-behavior-problems.md

@@ -10,7 +10,7 @@ issue:
 pages: 
 is_published: true
 image: /assets/images/papers/biol-psychiatry-cogn-neurosci-neuroimaging.png
-projects:
+projects: [abcd]
 tags: []
 
 # Text

papers/_posts/2020-02-04-poudel-common-and-distinct.md

@@ -10,7 +10,7 @@ issue:
 pages: 107884
 is_published: true
 image: /assets/images/papers/drug-alcohol-depend.png
-projects:
+projects: ["pace", "athena"]
 tags: [preprint]
 
 # Text

papers/_posts/2020-07-11-morawetz-multiple-largescale-neural.md

@@ -10,7 +10,7 @@ issue:
 pages: 382-395
 is_published: true
 image: /assets/images/papers/neurosci-biobehav-rev.png
-projects:
+projects: ["pace", "athena"]
 tags: []
 
 # Text

papers/_posts/2020-08-29-samartsidis-estimating-the-prevalence.md

@@ -10,7 +10,7 @@ issue:
 pages:
 is_published: true
 image: /assets/images/papers/res-synth-methods.png
-projects:
+projects: ["pace", "athena"]
 tags: []
 
 # Text

papers/_posts/2020-12-16-conley-altered-hippocampal-microstructure.md

@@ -0,0 +1,40 @@
+---
+layout: paper
+title: "Altered hippocampal microstructure and function in children who experienced Hurricane Irma"
+nickname: 2020-12-16-conley-altered-hippocampal-microstructure
+authors: "Conley MI, Skalaban LJ, Rapuano KM, Gonzalez R, Laird AR, Dick AS, Sutherland MT, Watts R, Casey BJ"
+year: "2020"
+journal: "Dev Psychobiol"
+volume: 
+issue: 
+pages: 
+is_published: true
+image: /assets/images/papers/dev-psychobiol.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: 
+preprint:
+supplement:
+
+# Links
+doi: "10.1002/dev.22071"
+pmid: 33325561
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+Hurricane Irma was the most powerful Atlantic hurricane in recorded history, displacing 6 million and killing over 120 people in the state of Florida alone. Unpredictable disasters like Irma are associated with poor cognitive and health outcomes that can disproportionately impact children. This study examined the effects of Hurricane Irma on the hippocampus and memory processes previously related to unpredictable stress. We used an innovative application of an advanced diffusion-weighted imaging technique, restriction spectrum imaging (RSI), to characterize hippocampal microstructure (i.e., cell density) in 9- to 10-year-old children who were exposed to Hurricane Irma relative to a non-exposed control group (i.e., assessed the year before Hurricane Irma). We tested the hypotheses that the experience of Hurricane Irma would be associated with decreases in: (a) hippocampal cellularity (e.g., neurogenesis), based on known associations between unpredictable stress and hippocampal alterations; and (b) hippocampal-related memory function as indexed by delayed recall. We show an association between decreased hippocampal cellularity and delayed recall memory in children who experienced Hurricane Irma relative to those who did not. These findings suggest an important role of RSI for assessing subtle microstructural changes related to functionally significant changes in the developing brain in response to environmental events.