update images

mfroeling · Feb 22, 2023 · 44e29ea · 44e29ea
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diff --git a/Gemfile.lock b/Gemfile.lock
@@ -17,7 +17,7 @@ GEM
     faraday-net_http (3.0.2)
     ffi (1.15.5-x64-mingw32)
     forwardable-extended (2.6.0)
-    google-protobuf (3.21.12-x64-mingw32)
+    google-protobuf (3.22.0-x64-mingw32)
     http_parser.rb (0.8.0)
     i18n (1.12.0)
       concurrent-ruby (~> 1.0)
@@ -66,10 +66,10 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rexml (3.2.5)
-    rouge (4.0.1)
+    rouge (4.1.0)
     ruby2_keywords (0.0.5)
     safe_yaml (1.0.5)
-    sass-embedded (1.57.1-x64-mingw32)
+    sass-embedded (1.58.3-x64-mingw32)
       google-protobuf (~> 3.21)
     sawyer (0.9.2)
       addressable (>= 2.3.5)

diff --git a/README.md b/README.md
@@ -1 +1,3 @@
+[![Netlify Status](https://api.netlify.com/api/v1/badges/ae8708c6-9ff0-44e2-b493-032c2184845c/deploy-status)](https://app.netlify.com/sites/qmritools/deploys)
+
 code to generate www.QMRITools.com website
diff --git a/_includes/page-image b/_includes/page-image
@@ -0,0 +1,16 @@
+{% comment %}
+*   
+*   Example: {% include page-image im_id=''%}
+*   
+{% endcomment %}
+
+{% assign id = include.im_id %}
+{% assign img = page.images | where: "image_id", id %}
+
+<div>
+{% for item in img %}
+	<p align="center">
+	<img src = "{{ site.urlimg }}{{ item.image_name }}" {% if item.image_title %}title = "{{ item.image_title }}"{% endif %} {% if item.image_alt %}alt = "{{ item.image_alt }}"{% endif %} width="90%"/>
+	</p><br>
+{% endfor %}
+</div>
diff --git a/pages/about_bio.md b/pages/about_bio.md
@@ -1,19 +1,25 @@
 ---
+
 layout: page
+permalink: /about/bio
+
 title: "Biography"
 subheadline: "Yes its all about me..."
 teaser: "Martijn Froeling"
-permalink: /about/bio
+
 header: no
+
+images:
+  - image_id: 'me'
+    image_name: 'Martijn Froeling.jpg'
+    image_title: 'Martijn Froeling'
+    image_alt: 'Martijn Froeling' 
+
 ---
 
 Martijn Froeling has done his master's (July 2009) in Biomedical Engineering at the Eindhoven University of Technology and Performed his PdD studies on Diffusion Tensor Imaging of the human forearm at the Amsterdam University Medical Center and the Eindhoven University of Technology under the supervision of Prof. Dr. Ir. Klaas Nicolay, Prof. Dr. Ir. Gustav Strijkers and Prof. Dr. Ir. Aart Nederveen. Since his Ph.D. (Oktober 2012) he has continued his work on quantitative MRI in various organs such as the brain, peripheral nerves, muscle, kidney, and heart. Since July 2012 he works at the High Field group of the University Medical Center focussing on coil and hardware development for 7T systems and multi-nuclei imaging and clinical studies into neuromuscular diseases. Throughout his career, he has developed and maintained [QMRITools](https://github.com/mfroeling/QMRITools) for Mathematica, a toolbox for quantitative analysis of magnetic resonance imaging data of muscle, nerve, and heart. In 2021, he was awarded an NWO Vidi grant. In this project, he will study the relation between muscle architecture, microstructure, and function using multiparametric quantitative MRI. 
 
-<p align="center"><img 
-src="/assets/images/Martijn Froeling.jpg" 
-title="Martijn Froeling"
-alt="Martijn Froeling"  
-width="75%" /></p>
+{% include page-image im_id="me" %}
 
 - [ORCID](https://orcid.org/0000-0003-3841-0497){:target="_blank"}
 - [Pubmed](https://pubmed.ncbi.nlm.nih.gov/?term=Froeling+M&sort=date&size=200){:target="_blank"}

diff --git a/pages/about_lic.md b/pages/about_lic.md
@@ -1,8 +1,12 @@
 ---
+
 layout: page
 permalink: /about/licence
+
 title: "QMRITools licence"
+
 header: no
+
 ---
 
 [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause){:target="_blank"}
@@ -21,5 +25,4 @@ you from committing patent infringement. So, before you do anything with
 this program, make sure that you have permission to do so not merely in
 terms of copyright, but also in terms of patent law.
 
-Some code in the NiiTools packages was based on
-<https://github.com/tomdelahaije/nifti-converter>
+Some code in the NiiTools packages was based on [nifti-converter](https://github.com/tomdelahaije/nifti-converter){:target="_blank"}
diff --git a/pages/about_main.md b/pages/about_main.md
@@ -1,10 +1,24 @@
 ---
+
 layout: page
+permalink: /about/
+
 title: "About QMRITools"
 subheadline: "a little bit of history"
 teaser: "If you used it, please cite us"
-permalink: /about/
+
 header: no
+
+images:
+  - image_id: 'proc'
+    image_name: 'processing.png'
+    image_title: 'Quantitative muscle MRI processing'
+    image_alt: 'Quantitative muscle MRI processing' 
+  - image_id: 'app'
+    image_name: 'applications of QMRITools.png'
+    image_title: 'Applications of QMRITools'
+    image_alt: 'Applications of QMRITools' 
+
 ---
 
 <p align="center">
@@ -39,11 +53,7 @@ and fitting, j-coupling simulations and more. It currently contains over
 450 custom functions (over 30.000 lines of code) complete with more than 750
 documentation pages and demonstrations for each toolbox.
 
-<p align="center"><img 
-src="/assets/images/processing.png" 
-title="Quantitative muscle MRI processing"
-alt="Quantitative muscle MRI processing"  
-width="85%" /></p>
+{% include page-image im_id="proc" %}
 
 ### Referencing
 
@@ -65,11 +75,7 @@ When using the toolbox please cite one of the following references:
 	[link](https://onlinelibrary.wiley.com/doi/full/10.1002/nbm.4119){:target="_blank"}
 
 
-<p align="center"><img 
-src="/assets/images/applications of QMRITools.png" 
-title="applications of QMRITools"
-alt="applications of QMRITools"  
-width="90%" /></p>
+{% include page-image im_id="app" %}
 
 
 ### Publications using QMRITools

diff --git a/pages/bids_entsuf.md b/pages/bids_entsuf.md
@@ -1,10 +1,12 @@
 ---
 
 layout: page
+permalink: /bids/ents_suffs/
+
 title: "Entities and suffixes"
 subheadline: "Naming conventions of entities and suffixes"
 teaser: "The boring stuff but usefull..."
-permalink: /bids/ents_suffs/
+
 header: no
 
 ---

diff --git a/pages/bids_filefol.md b/pages/bids_filefol.md
@@ -1,10 +1,12 @@
 ---
 
 layout: page
+permalink: /bids/files_folders/
+
 title: "Files and folders"
 subheadline: "Naming conventions of files and folders"
 teaser: "Muscle-BIDS file structure explained."
-permalink: /bids/files_folders/
+
 header: no
 
 ---

diff --git a/pages/bids_main.md b/pages/bids_main.md
@@ -1,12 +1,12 @@
 ---
 
 layout: page
-title: "Muscle-BIDS"
+permalink: /bids/
 
+title: "Muscle-BIDS"
 subheadline: "Why QMRITools uses Muscle-BIDS"
 teaser: "Muscle-BIDS is a work in progress..."
 
-permalink: /bids/
 header: no
 
 ---

diff --git a/pages/bids_qmri.md b/pages/bids_qmri.md
@@ -1,10 +1,12 @@
 ---
 
 layout: page
+permalink: /bids/qmritools/
+
 title: "QMRITools and Muscle-BIDS"
 subheadline: "How to use Muscle-BIDS in QMRITools"
 teaser: "Muscle-BIDS is a work in progress..."
-permalink: /bids/qmritools/
+
 header: no
 
 ---
@@ -13,20 +15,20 @@ Automated processing only works if all input data is well-curated and defined. T
 
 Currently, a config file for a dataset needs to be defined. This stores the data to be expected and in which form. Based on the data described the correct (pre-)processing scripts will be selected and performed. If expected data is not found the processing step will be skipped. Also, if the data is not described in the config it will be ignored. Future work will increase the level of automatization reducing the user-dependent input.
 
-## Muscle-BIDS config - WIP
+### Muscle-BIDS config - WIP
 
 The configuration file can be present on each level of the Muscle-BIDS dataset. The best way is to define one config file in the root of the dataset. However, when a config file is also placed on the subject of session level this is used ignoring the global config. This allows making subject- or session-specific exceptions. 
 An example of a config file for a dataset that contains Dixon, DWI and T2 data acquired over multiple stacks is given below:
 
 
-## Conversion of DICOM to raw Muscle-BIDS NIfTI - WIP
+### Conversion of DICOM to raw Muscle-BIDS NIfTI - WIP
 
 Putting data in a Muscle_BIDS data structure can be done manually, however, this can be very time-consuming. Therefore, `QMRITools` has some automated scripts that can do this. Conversion from Dicom to nifty can be done in many different ways and many tools exist. It is not needed to use the `QMRITools` functions for this. Currently, it is only tested for very specific acquisition protocols and custom studies custom scripts likely have to be written. Based on the existing scripts this should not be too difficult. 
 
 For Dicom to Nifti conversion, `QMRITools` uses dcm2niix which already converts most data to BIDS-compliant nifty (**function**: `BidsDcmToNii`). These conversions are stored in the source data folder `"raw"`. Next, a second script collects the needed data and converts, moves and renames it to Muscle-BIDS-compliant files and folders (**function**: `MuscleBidsConvert`). This is done based on the user-defined config file. Both function loop over all folders and ignore the ones already processed.
 
 
-## Processing of Muscle-BIDS data - WIP
+### Processing of Muscle-BIDS data - WIP
 
 If the dataset is set up properly and the config file is defined data processing of known data types is done fully automated (**function**: `MuscleBidsProcess`). The processing script will go through all folders finds the needed data and process all data for which the needed input is present. Data already processed will be skipped. Reprocessing of data can be forced for all data, data processed before a specific data or data processing with an old `QMRITools` version. To keep track of all this `QMRITools` creates additional `"*.json"` files with the suffix `"_check"`. If these files are not present data will be reprocessed. 
 
@@ -45,7 +47,7 @@ The following automated processing scripts are being developed:
 > - Automated per-muscle tractography.
 
 
-## Analysis of Muscle-BIDS data – WIP
+### Analysis of Muscle-BIDS data – WIP
 
 Based on the Muscle-BIDS outputs the generated qMRI parameters can be analyzed of used for muscle evaluation. Since every study has different needs it is highly unlikely that generalized scrips will become available. However, the following “general” scripts are being developed:
 

diff --git a/pages/contact.md b/pages/contact.md
@@ -2,11 +2,12 @@
 
 layout: page
 permalink: /contact/
-header: no
 
 title: "Contact"
 subheadline: 'Get in contact with the team'
 
+header: no
+
 ---
 
 Leave your message here and we will get in contact as soon as possible.

diff --git a/pages/contact_act.md b/pages/contact_act.md
@@ -2,11 +2,11 @@
 
 layout: page
 permalink: /contact/thanks/
-header: no
 
 title: "Thanks!"
 subheadline: 'Awesome, you reached out!'
 
+header: no
 
 ---
 

diff --git a/pages/doc_demo.md b/pages/doc_demo.md
@@ -1,14 +1,17 @@
 ---
+
 layout: page
+permalink: /doc/demo/
+
 title: "QMRITools demonstration"
 subheadline: "If you want examples... here the are"
 teaser: "If you need more contact us!"
-permalink: /doc/demo/
+
 header: no
+
 ---
 
-<a name="top"></a>
-The release and repository contains [a demo data sets and a demonstration file](https://github.com/mfroeling/QMRITools/tree/master/QMRITools/Resources)
+The release and repository contains [a demo data sets and a demonstration file](https://github.com/mfroeling/QMRITools/tree/master/QMRITools/Resources){:target="_blank"}
 in which there is a file `Demonstrations.nb` and a folder `DemoData`. 
 If the tool has been installed as a paclet the paclet folder conains the `Demonstrations.nb` which will automatically unpack the demo data. By default the
 `Demonstrations.nb` looks for the folders `DemoData` in the same

diff --git a/pages/doc_instal.md b/pages/doc_instal.md
@@ -1,11 +1,14 @@
 ---
+
 layout: page
+permalink: /doc/instal/
+
 title: "QMRITools installation"
 subheadline: "How to install QMRITools"
 teaser: "If it doesn't work, read again."
-permalink: /doc/instal/
 
 header: no
+
 ---
 
 

diff --git a/pages/doc_main.md b/pages/doc_main.md
@@ -1,22 +1,31 @@
 ---
 layout: page
+permalink: /doc/
+
 title: "Documentation and installation"
 subheadline: "How to use and install QMRITools"
 teaser: "I hope it helps..."
-permalink: /doc/
+
 header: no
+
+images:
+  - image_id: 'addon'
+    image_name: 'addons.PNG'
+    image_title: 'QMRITools package add on'
+    image_alt: 'QMRITools package add on' 
+  - image_id: 'guide'
+    image_name: 'Guide.PNG'
+    image_title: 'Guides QMRITools mathematica documentation'
+    image_alt: 'Guides QMRITools mathematica documentation' 
+
 ---
 
-<a name="top"></a>
 The toolbox always works within the latest version of 
 Mathematica and does not support any backward
 compatibility. After the toolbox is installed correctly it should show
 up as a package in the Mathematica add-ons.
 
-<p align="center">
-<img src="/assets/images/addons.PNG" alt="QMRITools package add on"  width="80%" />
-</p>
-
+{% include page-image im_id="addon" %}
 
 ### Installation
 
@@ -34,6 +43,4 @@ A notebook with all functions and their description can be found [here](https://
 Documentation of all functions and their options is fully integrated in the Mathematica documentation. An online version of the full documentation can be 
 found [here](../assets/htmldoc/html/guide/qmritools){:target="_blank"}.
 
-<p align="center">
-<img src="/assets/images/Guide.PNG" alt="Guides QMRITools mathematica documentation"  width="80%" />
-</p>
+{% include page-image im_id="guide" %}
Original file line number	Diff line number	Diff line change
		@@ -1 +1,3 @@
		[![Netlify Status](https://api.netlify.com/api/v1/badges/ae8708c6-9ff0-44e2-b493-032c2184845c/deploy-status)](https://app.netlify.com/sites/qmritools/deploys)

		code to generate www.QMRITools.com website