Merge pull request #1 from vsoch/fix/dead-links

fixing dead links

Gemfile

@@ -0,0 +1,5 @@
+source "https://rubygems.org"
+
+#gem "rails"
+gem 'github-pages'
+gem 'jekyll'

_config.yml

@@ -8,9 +8,9 @@ highlighter:      rouge
 
 paginate: 20
 paginate_path: "page:num"
-baseurl: /
+baseurl: /v1/
 domain_name: 'vsoch.github.io'
-google_analytics: 'UA-67197905-1'
+# google_analytics: 'UA-67197905-1'
 disqus: true
 disqus_shortname: 'vsoch'
 

_layouts/default.html

@@ -6,15 +6,15 @@
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
   <title>{{ site.name }}{% if page.title %} - {{ page.title }}{% endif %}</title>
-  <link rel="shortcut icon" href="https://vsoch.github.io/assets/images/favicon.ico">
-  <link rel="stylesheet" href="https://vsoch.github.io/assets/css/bootstrap.min.css">
-  <link rel="stylesheet" href="https://vsoch.github.io/assets/css/style.css">
+  <link rel="shortcut icon" href="https://vsoch.github.io/v1/assets/images/favicon.ico">
+  <link rel="stylesheet" href="https://vsoch.github.io/v1/assets/css/bootstrap.min.css">
+  <link rel="stylesheet" href="https://vsoch.github.io/v1/assets/css/style.css">
   <link rel="alternate" type="application/rss+xml" title="VSoch" href="{{ site.baseurl }}rss.xml">
-  <link rel="stylesheet" href="https://vsoch.github.io/assets/css/highlight.css">
+  <link rel="stylesheet" href="https://vsoch.github.io/v1/assets/css/highlight.css">
   <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css">
-  <script src="https://vsoch.github.io/assets/js/jekyll-search.min.js" type="text/javascript"></script>
+  <script src="https://vsoch.github.io/v1/assets/js/jekyll-search.min.js" type="text/javascript"></script>
   <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
-  <script src="https://vsoch.github.io/assets/js/toc.js" type="text/javascript"></script>
+  <script src="https://vsoch.github.io/v1/assets/js/toc.js" type="text/javascript"></script>
   {% seo %}
 
 </head>
@@ -54,9 +54,9 @@ <h2>Recent Posts</h2>
   </section>
   </div>
 
-  <script src="https://vsoch.github.io/assets/js/main.js"></script>
-  <script src="https://vsoch.github.io/assets/js/highlight.js"></script>
-  <script src="https://vsoch.github.io/assets/js/bootstrap.min.js"></script>
+  <script src="https://vsoch.github.io/v1/assets/js/main.js"></script>
+  <script src="https://vsoch.github.io/v1/assets/js/highlight.js"></script>
+  <script src="https://vsoch.github.io/v1/assets/js/bootstrap.min.js"></script>
   <script>hljs.initHighlightingOnLoad();</script>
 
   <script>

_posts/2015-09-13-nifti-drop.md

@@ -14,7 +14,7 @@ The biggest challenge with developing tools for neuroimaging researchers is the
 I want to be able to do the smaller stuff in my web-browser. It's amazing how many posts I see on different neuroimaging lists about doing basic operations with headers or the data, and visualization is so low priority that nobody gives it the time of day. One of my favorite things to do is develop web-based visualizations. [Most of my work](http://www.github.com/vsoch/pybraincompare) relies on some python backend to do stuff first, and then render with web-stuffs. I also tried making a small app to [show local images in the browser](http://www.npmjs.com/package/brain-browser), or as a default [directory view](https://github.com/vsoch/niindex). But this isn't good enough. I realized some time ago that these tools are only going to be useful if they are drag and drop. I want to be able to load, view header details, visualize in a million cool ways, and export different manipulations of my data without needing to clone a github repo, log in anywhere, or do anything beyond dragging a file over a box. So this weekend, I started some basic learning to figure out how to do that. This is the start of Nifti-drop:
 
 
-<img src="/assets/images/posts/nifti-drop/nifti-drop.png" style="width:100%">
+<img src="/v1/assets/images/posts/nifti-drop/nifti-drop.png" style="width:100%">
 #[DEMO](http://vsoch.github.io/nifti-drop)  
 
 

_posts/2015-12-21-artbrain.md

@@ -7,15 +7,15 @@ tags: art
 
 Got Santa on the Brain? We do at Poldracklab! Ladies and gentlemen, we start with a nice square Santa:
 
-<img src="/assets/images/posts/artbrain/santa-512.png" style="width:50%">
+<img src="/v1/assets/images/posts/artbrain/santa-512.png" style="width:50%">
 
 We convert his colors to integer values...
 
-<img src="/assets/images/posts/artbrain/santa_int.png" style="width:100%">
+<img src="/v1/assets/images/posts/artbrain/santa_int.png" style="width:100%">
 
 And after we do some substantial research on the [christmas spirit network](http://www.bmj.com/content/351/bmj.h6266), we use our brain science skills and...
 
-<img src="/assets/images/posts/artbrain/santa.png" style="width:100%">
+<img src="/v1/assets/images/posts/artbrain/santa.png" style="width:100%">
 
 We've found the Christmas Spirit Network! 
 
@@ -108,4 +108,4 @@ Finally, since we want to map this onto a brain image (that doesn't support diff
 
 For the final brain map, I normalized to a Z score to give positive and negative values, because then using the [Papaya Viewer](https://github.com/rii-mango/Papaya) the default will detect these positive and negative, and give you two choices of color map to play with. Check out an [example here](https://vsoch.github.io/artbrain), or just [follow instructions](https://github.com/vsoch/artbrain#installation) to make one yourself!  I must admit I threw this together rather quickly, and only tested on two square png images, so be on the lookout for them bugs. Merry Christmas and Happy Holidays from the Poldracklab! We found Santa on the brain, methinks.
 
-<img src="/assets/images/posts/artbrain/goggles.png" style="width:100%">
+<img src="/v1/assets/images/posts/artbrain/goggles.png" style="width:100%">

_posts/2015-12-5-brainart.md

@@ -23,15 +23,15 @@ This is closer to a "true" data image because it was generated from actual brain
 
 You can skip over everything and just look at the <a href="http://vsoch.github.io/brainart">gallery</a>, or the <a href="http://www.github.com/vsoch/brainart">code</a>. It's under development and there are many things I am not happy with (detailed below), but it does pretty well for this early version. For example, here is "The Scream":
 
-<img src="/assets/images/posts/brainart/screamblack.png" style="width:100%">
+<img src="/v1/assets/images/posts/brainart/screamblack.png" style="width:100%">
 
 This isn't just any static image. Let's look a little closer...
 
-<img src="/assets/images/posts/brainart/scream2.png" style="width:100%">
+<img src="/v1/assets/images/posts/brainart/scream2.png" style="width:100%">
 
 Matter of fact, each "pixel" is a tiny brain:
 
-<img src="/assets/images/posts/brainart/scream3.png" style="width:100%">
+<img src="/v1/assets/images/posts/brainart/scream3.png" style="width:100%">
 
 And when you see them <a href="http://vsoch.github.io/brainart">interactively</a>, you can click on any brain to be taken to the data from which it was generated in the NeuroVault database. BrainArt!
 
@@ -46,7 +46,7 @@ UPDATE 12/6/2015: The color tables were extended to include brainmaps of single
 
 The generation could still be optimized. It's really slow. Embarrassingly, I have <a href="https://github.com/vsoch/brainart/blob/master/brainart/utils.py#L89">for loops</a>. The original implementation did not generate x and y to match the specific sampling rate specified by the user, and this has also been fixed.
 
-<img src="/assets/images/posts/brainart/girl_with_pearl_black.png" style="width:100%">
+<img src="/v1/assets/images/posts/brainart/girl_with_pearl_black.png" style="width:100%">
 
 I spent an entire weekend doing this, and although I have regrets about not finishing "real" work, this is pretty awesome. I should have more common sense and not spend so much time on something no one will use except for me... oh well! It would be fantastic to have different color lookup tables, or even sagittal and/or coronal images. Feel free to contribute if you are looking for some fun! :)
 
@@ -107,4 +107,4 @@ brainart --input /home/vanessa/Desktop/flower.jpg --sample 100
 ## Contribute!
 The [gallery](http://vsoch.github.io/brainart) is the index file hosted on the github pages for this repo. See [instructions](https://github.com/vsoch/brainart#gallery) for submitting something to the gallery. While I don't have a server to host generation of these images dynamically in the browser, something like this could easily be integrated into [NeuroVault](http://www.neurovault.org) for users to create art from their brainmaps, but methinks nobody would want this except for me :)
 
-<img src="/assets/images/posts/brainart/spiderman_zoom1.png" style="width:100%">
+<img src="/v1/assets/images/posts/brainart/spiderman_zoom1.png" style="width:100%">