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2_GettingStarted.txt
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2_GettingStarted.txt
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/**
\page Getting_Started Getting Started
For Download/Installation Instructions, please see the following:
- [Download Instructions](Download.html)
- [Installation Instructions](Installation.html)
For Frequently Asked Questions, please see the dedicated [FAQ](FAQ.html) section.
FeTS has been designed as a modular platform, currently incorporating components for:
-# User interaction (e.g., coordinate definition, region annotation, and spherical approximation of abnormalities)
- \ref gs_imageLoading
- \ref gs_imageVisualization
- \ref gs_tabDocking
- \ref gs_utilities
- \ref gs_drawing
- \ref gs_keyboard
-# \ref gs_preprocessing (e.g., smoothing, bias correction, co-registration, normalization)
-# \ref gs_segmentation
The components of interaction and pre-processing are available for all integrated applications giving a researcher (whether clinical or computational) a single point of entry and exit for all their tasks.
The following sections give a high-level overview of FeTS, with the intention of familiarizing a new user with the platform functionalities and interface.
\tableofcontents
--------
\section gs_FAQ Frequently Asked Questions
Please see the dedicated [FAQ](FAQ.html) section.
--------
\section gs_supportedImages Supported Images
Currently, FeTS supports visualization of <b>MR, CT, PET, X-Ray and Full-field Digital Mammography (FFDM) </b> images in both NIfTI (i.e., <b>.nii</b>, <b>.nii.gz</b>) and DICOM (i.e., <b>.dcm</b>) formats. For MRI, the following modalities are currently supported (the image modality box equivalent is shown in parenthesis):
| Acronym | Image Type |
|:-----------:|:---------------------------------------------------------------------:|
| T1 | Native T1-weighted MR Image |
| T1Gd | Post-contrast T1-weighted MR Image (also known as T1c, T1-CE) |
| T2 | Native T2-weighted MR Image |
| FLAIR | T2-weighted Fluid Attenuated Inversion Recovery MR Image |
| DSC-ap-rCBV | automatically-extracted proxy to relative Cerebral Blood Volume |
| PERFUSION | Dynamic Susceptibility Contrast-enhanced MR Image (also known as DSC) |
| DTI | Diffusion Tensor Image |
| DWI | Diffusion Weighted Image |
| REC | Recurrence Maps |
<b>*</b> These modalities are currently visualized only within the "Confetti" application.
In addition, FeTS offers the ability to extract and visualize commonly used measurements from DTI [1] and DSC-MRI, while accounting for leakage correction [2]. The exact measurements supported are:
| Acronym | Image Type |
|:-----------:|:---------------------------------------------------------------:|
| DTI-FA | Fractional Anisotropy |
| DTI-AX | Axial Diffusivity |
| DTI-RAD | Radial Diffusivity |
| DTI-TR | Trace |
| DSC-ap-rCBV | automatically-extracted proxy to relative Cerebral Blood Volume |
| DSC-PH | Peak Height |
| DSC-PSR | Percentage Signal Recovery |
--------------------------------------------------------------------
References:
-# J.M.Soares, P.Marques, V.Alves, N.Sousa. "A hitchhiker's guide to diffusion tensor imaging", Front Neurosci. 7:31, 2013. DOI: 10.33
fnins.2013.00031
-# E.S.Paulson, K.M.Schmainda, "Comparison of dynamic susceptibility-weighted contrast-enhanced MR methods: recommendations for measuring relative cerebral blood volume in brain tumors", Radiology. 249(2):601-613, 2008. DOI: 10.1148/radiol.2492071659
--------
\section gs_imageLoading Image Loading
The <b>File -> Load</b> menu is used to load all image types.
\image html imageLoading_resize.png "Loading images for visualization/processing"
\image latex imageLoading_resize.png "Loading images for visualization/processing"
--------
For every loaded NIfTI image, the modality is automatically assigned using information from the filename. To <b> assign modalities </b> for DICOM images, or in case of a discrepancy in the modality of a NIfTI image, the user can use the drop-down modality switcher (see below) to revise the modality accordingly. This is typically needed in the <a href="ht_SpecialApps.html">Specialized Applications</a>.
\image html modalities_resize.png "Modality switching for individual images"
\image latex modalities_resize.png "Modality switching for individual images"
--------
\section gs_imageVisualization Image Visualization
Sliders on each visualization panel (highlighted in green in the figure below) control the movement across respective axes. Note that in DSC-MRI, the single horizontal slider (highlighted in yellow) moves across the time of the acquired dynamic scan.
<br>
Various adjustments are available to the user, including:
-# contrast/brightness: right mouse button click + horizontal/vertical drag on any visualization panel, respectively.
-# windowing of intensities and setting of different visualization type: bottom-right panel.
-# zooming into the image via Ctrl + mouse wheel.
The bottom-left panel of FeTS (highlighted in red) shows basic information about the image and the position of the cross-hair. In the visualization panes, the "Z" axis is the center; and "Y" and "X" are to its left and right, respectively. "Z" represents the Axial view for RAI-to-LPS images.
\image html sliders_resize.png "Visualization Sliders and Image Information"
\image latex sliders_resize.png "Visualization Sliders and Image Information"
The "Overlay" functionality enables the visualization between two loaded images:
-# Double-click one of the two images you want to visualize and then click on its corresponding "overlay" radio button, on its right-most column.
-# Click on the "overlay" radio button of the second image that you want to visualize.
-# Both "Overlay" and "Underlay" images are now visualized with 50% opacity.
-# Check the tick box "Change Opacity".
-# Moving the slider changes the opacity between the "Overlay" and the "Underlay" images.
The "Comparison Mode" puts the loaded images (3 maximum) side-by-side for easy visualization along the same axis.
\image html comparisonMode.png "Comparison Mode visualization"
\image latex comparisonMode.png "Comparison Mode visualization"
--------
\section gs_tabDocking Tab Docking (Windows-only)
Double clicking on the tab bar will dock/undock the entire section, resulting in larger visualization panels in your monitor. This behavior is replicated by single click of the dock/undock button at the end of the section as well.
\image html dock_comparison_resize.png "Left is while dock is active and right is undocked behavior"
\image latex dock_comparison_resize.png "Left is while dock is active and right is undocked behavior"
--------------------------------------------------------------------
References:
-# A.Gooya, K.M.Pohl, M.Billelo, G.Biros, C. Davatzikos, "Joint segmentation and deformable registration of brain scans guided by a tumog rowth model", Med Image Comput Comput Assist Interv. 14(Pt 2):532-40, 2011. DOI:10.1007/978-3-642-23629-7_65
-# A.Gooya, K.M.Pohl, M.Bilello, L.Cirillo, G.Biros, E.R.Melhem, C.Davatzikos, "GLISTR: glioma image segmentation and registration", IEET rans Med Imaging. 31(10):1941-54, 2012. DOI:10.1109/TMI.2012.2210558
-# D.Kwon, R.T.Shinohara, H.Akbari, C.Davatzikos, "Combining Generative Models for Multifocal Glioma Segmentation and Registration", MeI mage Comput Comput Assist Interv. 17(Pt 1):763-70, 2014. DOI:10.1007/978-3-319-10404-1_95
-# S.Bakas, K.Zeng, A.Sotiras, S.Rathore, H.Akbari, B.Gaonkar, M.Rozycki, S.Pati, C.Davatzikos, "Segmentation of gliomas in multimodam agnetic resonance imaging volumes based on a hybrid generative-discriminative framework", In Proc. Multimodal Brain Tumor Segmentation (BraTS) Challenge. 4:5-12, 2015.
-# S.Bakas, K.Zeng, A.Sotiras, S.Rathore, H.Akbari, B.Gaonkar, M.Rozycki, S.Pati, C.Davatzikos, "GLISTRboost: combining multimodal MRs egmentation, registration, and biophysical tumor growth modeling with gradient boosting machines for glioma segmentation", Brainlesion (2015). 9556:144-155, 2016. DOI:10.1007/978-3-319-30858-6_1
-# S.Bakas, H.Akbari, A.Sotiras, M.Bilello, M.Rozycki, J.Kirby, J.Freymann, K.Farahani, C.Davatzikos, "Advancing The Cancer Genome Atlag lioma MRI collections with expert segmentation labels and radiomic features", Nature Scientific Data 4:170117, 2017. DOI:10.103s data.2017.117
-# D.Kwon, M.Niethammer, H.Akbari, M.Bilello, C.Davatzikos, K.M.Pohl, "PORTR: Pre-Operative and Post-Recurrence Brain Tumor Registration", IEEE Trans Med Imaging. 33(3):651-667, 2014. DOI:10.1109/TMI.2013.2293478
--------
\section gs_drawing Label Annotation/Drawing Panel
This panel provides the ability to annotate Regions of Interest (ROIs) and save them as masks.
\image html drawing_resize.png "Drawing functions"
\image latex drawing_resize.png "Drawing functions"
While drawing, you can switch across the image volumes loaded in FeTS, by pressing the numbers 1-9 on your keyboard.
Toggle between non-zero (taken from the opacity box) and zero opacity of the entire annotated mask by using the keyboard key "m".
Visualize a single label using "Control + <label number>" and add labels to the visualization using "Alt + <label number>". To reset, press "Control/Alt + 0".
There are the following controls underneath the <b>Drawing</b> tab:
| Button/Box | Description |
|:--------------------:|:----------------------------------------------------------------------------------------------------------------------------------------:|
| View Mode | Switch from drawing mode (which is enabled when either Near or Far ROI drawing is selected) to normal viewing mode |
| Line | Draw a line of selected label color and size |
| Rectangle | Draw a rectangle of selected label color and size |
| Circle | Draw a circle of selected label color and size |
| Sphere | Draw a sphere of selected label color and pre-determined size from the size combo-box |
| Free-Hand | Draw selected label using brush of specified size using mouse left button drag |
| Fill | Fill a closed boundary with selected label - uses ITK's connected component filter |
| Eraser | Erases all labels using brush of specified size |
| Label Selector | Label selector between 1-9 |
| Marker Size | A square marker of specific voxel size |
| Marker Opacity | Sets the opacity of the marker between 0.0 (transparent) and 1.0 (opaque) |
| Clear Selected Label | Remove selected label completely from the mask |
| Clear All Labels | Remove all labels completely from the mask |
| Undo | By providing the same number of old and new values in the format AxBxC, the values of the annotated region can be quickly changed |
| Change Values | By providing the same number of old and new values in the format <b>AxBxC</b>, the values of the annotated region can be quickly changed |
--------
\section gs_keyboard Keyboard Shortcuts
These are the keyboard shortcuts available on FeTS:
| Key Stroke | Function/Action |
|:---------------:|:--------------------------------------------------------------------------:|
| 1-9 | [IMAGES] Show selected image from table |
| "m" | [DRAWING] Show/Hide all regions; picks up last used opacity |
| Control + 1-9 | [DRAWING] Only show selected label |
| Alt + 1-9 | [DRAWING] Add selected label to visualization |
| Control/Alt + 0 | [DRAWING] Reset label visualization; i.e., show all |
| Shift + Space | [SEED POINT] Set initial tumor center |
| Control + Space | [SEED POINT] Update tumor radius; on macOS, this is "Fn + Command + Space" |
| Space | [SEED POINT] Update tumor center |
--------
\section gs_utilities Utilities (Command-line only)
To make pipeline construction using FeTS easier, a bunch of utilities have been provided. They include
-# Resizing
-# DICOM conversion
-# Sanity checking
-# Image header information
-# Unique values in image
-# Changing pixel values.
For full details, run the command:
\verbatim
Utilities.exe -u
\endverbatim
--------
\section gs_preprocessing Pre-processing
Image pre-processing is essential to quantitative image analysis. FeTS pre-processing tools available under the "Preprocessing" menu are fully-parameterizable and comprise:
-<b>Denoising.</b> Intensity noise reduction in regions of uniform intensity profile is offered through a low-level image processing method, namely Smallest Univalue Segment Assimilating Nucleus (SUSAN) [1]. This is a custom implementation and does <b>NOT</b> call out to the original implementation distributed by FSL.
-<b>Co-registration.</b> Registration of various images to the same anatomical template, for examining anatomically aligned imaging signals in tandem and at the voxel level, is done using the Greedy Registration algorithm [5].
-<b>Bias correction.</b> Correction for magnetic field inhomogeneity is provided using a non-parametric non-uniform intensity normalization [2].
-<b>Intensity normalization.</b> Conversion of signals across modalities to comparable quantities using histogram matching [4].
-<b>Z-Scoring normalization.</b> Images are normalized using a z-scoring mechanism with option to do the normalization within the region of interest or across the entire image. In addition, there is an option to remove outliers & noise from the image by removing a certain percentage of the top and bottom intensity ranges [6].
-<b>Histogram Matching</b>
-<b>Skull Stripping (Deep Learning based)</b>
-<b>Mammogram Pre-processing</b>
<B>NOTE:</B> An extended set of algorithms are available via the command line utility <b>Preprocessing</b>. For full details, run the command:
\verbatim
Preprocessing.exe -u
\endverbatim
\image html pre-processing_resize.png "Available pre-processing algorithms"
\image latex pre-processing_resize.png "Available pre-processing algorithms"
<br>
--------------------------------------------------------------------
References:
-# S.M.Smith, J.M.Brady, "SUSAN - a new approach to low level image processing", Int. J. Comput. Vis. 23(1):45-78, 1997. DOI:10.102A :1007963824710
-# N.J.Tustison, B.B.Avants, P.A.Cook, Y.Zheng, A.Egan, P.A.Yushkevich, J.C.Gee, "N4ITK: Improved N3 Bias Correction", IEEE Trans MeI maging. 29(6):1310-20, 2010. doi: 10.1109/TMI.2010.2046908
-# S.Bauer, L.P.Nolte, M.Reyes, "Skull-stripping for Tumor-bearing Brain Images", arXiv. abs/1204.0357, 2012.
-# L.G.Nyul, J.K.Udupa, X.Zhang, "New Variants of a Method of MRI Scale Standardization", IEEE Trans Med Imaging. 19(2):143-50, 2000D OI:10.1109/42.836373
-# P.A.Yushkevich, J.Pluta, H.Wang, L.E.Wisse, S.Das, D.Wolk, "Fast Automatic Segmentation of Hippocampal Subfields and Medical Temporal Lobe Subregions in 3 Tesla and 7 Tesla MRI, Alzheimer's & Dementia: The Journal of Alzheimer's Association, 12(7), P126-127
-# T.Rohlfing, N.M.Zahr, E.V.Sullivan, A.Pfefferbaum, "The SRI24 multichannel atlas of normal adult human brain structure", Human Brain Mapping, 31(5):798-819, 2010. DOI:10.1002/hbm.20906
--------
\section gs_segmentation Segmentation
Currently there are two ways to produce segmentation labels for various structures in the images that are loaded:
-# using the Geodesic Distance Transform
-# using ITK-SNAP
-# Skull Stripping (Deep Learning based)
-# Tumor Segmentation (Deep Learning based)
\image html applicationsSeg_resize.png "Segmentation applications"
\image latex applicationsSeg_resize.png "Segmentation applications"
More information on how to run those is provided in the <a href="ht_Segmentation.html">corresponding How-To section</a>.
--------
\section gs_commandLineUsage Command Line Usage
Almost every application offered by FeTS can be used from the command line and utilizing the FeTS's powerful command line APIs is relatively straight-forward. The following parameters are present in every CLI:
| Laconic | Verbose | Function/Action |
|:-------:|:-------:|:--------------------------------------------------------------------------------------------:|
| u | usage | Usage message giving all the possible parameters of an application |
| h | help | Help message giving details of parameters (including defaults and ranges) with some examples |
| v | version | The version information of the application |
An example to show the verbose help for an application called <b>${Application}</b>:
| Platform (x64) | Command |
|:--------------:|:--------------------------------------------------------------------------------:|
| Windows | ${FeTS_InstallDir}/bin/${ApplicationName}.exe -h |
| Linux | ${FeTS_InstallDir}/bin/${ApplicationName} -h |
| macOS | ~/Applications/FeTS_${version}.app/Contents/Resources/bin/${ApplicationName} -h |
Detailed explanation of using the command line is available in the \ref How_To_Guides.
--------
*/
/**
\page FAQ Frequently Asked Questions
\tableofcontents
\section gs_FAQ_1 Which platforms are supported by FeTS installers?
| Platform (x64) | Tested | Unsupported |
|:--------------:|:------------------------------------------------------:|:----------------------:|
| Windows | 7, 8, 10 | XP, Vista |
| Linux | Ubuntu 16.04, 18.04; Debian 9, CentOS 7 (source build) | Ubuntu 14.04; CentOS 6 |
| macOS | 10.13, 10.14 | 10.12 |
\section gs_FAQ_2 How do I run FeTS Applications from the Command Line?
- The full list of command line applications available is shown by running the following command (pretty much every application is available via the command line):
\verbatim
${FeTS_InstallDir}/bin/FeTS -h
\endverbatim
- An exemplary scenario to run Applications from the command line (the example shown is to get verbose help):
| Platform (x64) | Functionality | Successful Installation | Build From Source (after invoking "make install") | FUSE Issues (after invoking "--appimage-extract") |
|:--------------:|:-----------------:|:--------------------------------------------------------------------------------:|:-------------------------------------------------:|:-------------------------------------------------:|
| Windows | Generic | ${FeTS_InstallDir}/bin/${ApplicationName}.exe -h | ${FeTS_InstallDir}/bin/${ApplicationName}.exe -h | N.A. |
| Linux | Generic | ${FeTS_InstallDir}/bin/fets ${FeTS_InstallDir}/bin/${ApplicationName}.cwl -h | ${FeTS_InstallDir}/bin/${ApplicationName} -h | ~/FeTS/${version}/${ApplicationName} -h |
| macOS | Generic | ~/Applications/FeTS_${version}.app/Contents/Resources/bin/${ApplicationName} -h | ${FeTS_InstallDir}/bin/${ApplicationName} -h | N.A. |
| Windows | FeatureExtraction | ${FeTS_InstallDir}/bin/FeatureExtraction.exe -h | ${FeTS_InstallDir}/bin/FeatureExtraction.exe -h | N.A. |
| Linux | FeatureExtraction | ${FeTS_InstallDir}/bin/fets FeatureExtraction.cwl -h | ${FeTS_InstallDir}/bin/FeatureExtraction -h | ~/FeTS/${version}/FeatureExtraction -h |
| macOS | FeatureExtraction | ~/Applications/FeTS_${version}.app/Contents/Resources/bin/FeatureExtraction -h | ${FeTS_InstallDir}/bin/FeatureExtraction -h | N.A. |
- There are detailed examples of individual command line usage in the [How To](How_To_Guides.html) section of the documentation.
\section gs_FAQ_3 What are the OpenGL requirements to run FeTS?
- If FeTS is unable to load images or you receive the error about minimum OpenGL version wasn't found, please update your display drivers in order to have **OpenGL version 3.2 or above**. Some useful resources:
- OpenGL update for Ubuntu [[ref](https://www.phoronix.com/scan.php?page=news_item&px=Ubuntu-16.04-OI-Intel-GL-4.2)]:
\verbatim
sudo apt-add-repository ppa:oibaf/graphics-drivers && sudo apt-get update && sudo apt-get dist-upgrade
\endverbatim
- https://community.khronos.org/t/how-to-update-opengl/75314
- https://ubuntuforums.org/showthread.php?t=2326268
- https://www.techwalla.com/articles/how-to-update-opengl-drivers
- [A reply to a related issue](https://github.com/CBICA/FeTS/issues/654#issuecomment-543744366):
\verbatim
MESA_GL_VERSION_OVERRIDE=4.5 #put the opengl version you want to use here
\endverbatim
\section gs_FAQ_4 What if I am having issues with the Linux Installer?
This section highlights some of the common issues on Linux machines.
\subsection gs_FAQ_4_1 FUSE Issues
If the installer successfully finishes and you are not able to run FeTS due to FUSE issues, please extract the installer using the following command to extract the contents of the AppImage onto the hard drive:
\verbatim
user@pc:~# ~/FeTS/${version}/fets --appimage-extract
\endverbatim
- This will extract the package to the path `~/FeTS/${version}/squashfs-root/usr/` with the binaries present in `~/FeTS/${version}/squashfs-root/usr/bin`.
- To run **FeTS** from the command line in this manner, the user would need to make the following additions:
- Add the path `~/FeTS/${version}/squashfs-root/usr/lib` to their environment variable **PATH**: `export PATH=~/FeTS/${version}/squashfs-root/usr/bin:$PATH`
- Add the path `~/FeTS/${version}/squashfs-root/usr/lib` to their environment variable **LD_LIBRARY_PATH**: `export LD_LIBRARY_PATH=~/FeTS/${version}/squashfs-root/usr/lib:$LD_LIBRARY_PATH`
- This will need to be present in the user's shell start up file `.bashrc`, `.cshrc`, `.profile`, `.kshrc`, etc.` for the settings to be persistent across login sessions.
- All the command line applications should now be available for use. For example:
\verbatim
FeatureExtraction \ # the executable should already be in the $PATH
-n AAC0_timestamp \ # this is the subject ID for this run
-i /usr/path/T1.nii.gz,/usr/path/T2.nii.gz -t T1,T2 \ # the co-registered input image(s) and their respective modalities
-m /user/path/mask.nii.gz \ # the mask file (co-registered with the input image(s)
-r 2,4,5 -l ED,EN,NE \ # the labels from the mask file from where features need to be extracted and their respective label identifier(s)
-p /usr/path/features.csv \ # the parameter file to use
-o /usr/path/output.csv # the path to write the output
\endverbatim
\subsection gs_FAQ_4_2 GLIBCXX or GLIBC Issues
- This is happening because the Linux binaries are compiled using the [GCC-4.8 package on Ubuntu 16.04](https://packages.ubuntu.com/xenial/gcc-4.8); therefore you will need to update GCC 4.8.5 or newer in order to get FeTS to work. Some examples are shown:
- Ubuntu [[ref](https://askubuntu.com/a/581497)]:
\verbatim
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-4.9 g++-4.9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9
\endverbatim
- CentOS [[ref](https://www.softwarecollections.org/en/scls/user/rhscl/?search=devtoolset&policy=&repo=&order_by=-create_date&per_page=10)]:
\verbatim
sudo yum install centos-release-scl
sudo yum install devtoolset-6
\endverbatim
- You can still build FeTS from source using the instructions in [Technical Reference](Technical_Reference.html). Note that you will need a [C++11 compliant compiler](https://en.cppreference.com/w/cpp/compiler_support#cpp11).
\section gs_FAQ_5 Is there a minimum recommended screen resolution for running FeTS?
The minimum recommended resolution is 1200x1024. We have seen some visualization issues with high DPI (>2K) screens and bug reports related to it will be appreciated.
\section gs_FAQ_6 Where can I find the FeTS Docker Image?
You can find all the builds in our Docker Hub repository: https://hub.docker.com/r/cbica/fets
\section gs_FAQ_7 How do I run the FeTS Docker Image to show the interface?
\verbatim
docker run -it \
-v /tmp/.X11-unix:/tmp/.X11-unix \
-v $(pwd)/test:/app \
-e DISPLAY=$DISPLAY \
-u qtuser \
cbica/fets
\endverbatim
\section gs_FAQ_8 What if I am having an issue not listed here?
Please [open a new issue](https://github.com/CBICA/FeTS/issues/new?assignees=&labels=&template=bug-report.md&title=) with us and we will do our best to resolve it.
*/