diff --git a/5_TechReference.txt b/5_TechReference.txt index b84ecb7c8..49aa1af6b 100644 --- a/5_TechReference.txt +++ b/5_TechReference.txt @@ -386,12 +386,6 @@ An example of the list of commands to run to compile CaPTk and its dependencies: \verbatim git clone https://github.com/CBICA/CaPTk.git cd CaPTk -mkdir bin -cd bin -#git lfs fetch --all # downloads all the precompiled binaries for different applications and Qt with the required installation options -# change ${platform} to either windows, linux or macos (case sensitive) -wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/${platform}.zip -O precompiledApps.zip -wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/${platform}.zip -O qt.zip git submodule update --init --recursive # this ensures all submodules are initialized and up-to-date mkdir build # this is where we will build all the binaries cd build diff --git a/CMakeLists.txt b/CMakeLists.txt index 71d6a28d4..6ccf2f6b6 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -13,7 +13,7 @@ SET( ${PROJECT_NAME}_Variant "Full" ) # the particular variant of CaPTk (Full/Ne SET( PROJECT_VERSION_MAJOR 1 ) SET( PROJECT_VERSION_MINOR 8 ) -SET( PROJECT_VERSION_PATCH 0.nonRelease ) +SET( PROJECT_VERSION_PATCH 0.Alpha3 ) SET( PROJECT_VERSION_TWEAK ) # check for the string "nonRelease" in the PROJECT_VERSION_PATCH variable diff --git a/docs/1_credits.html b/docs/1_credits.html index 36f56b93d..cd8592d24 100644 --- a/docs/1_credits.html +++ b/docs/1_credits.html @@ -12,7 +12,7 @@

- Cancer Imaging Phenomics Toolkit (CaPTk) v.1.8.0.Alpha2  | Contact: software@cbica.upenn.edu + Cancer Imaging Phenomics Toolkit (CaPTk) v.1.8.0.Alpha3  | Contact: software@cbica.upenn.edu
Disclaimer: CaPTk has been designed for non-commercial research purposes only and has not been reviewed or approved by the Food and Drug Administration (FDA). It is not intended or recommended for clinical application.
diff --git a/docs/BreastCancer_LIBRA.html b/docs/BreastCancer_LIBRA.html index 1f0bd1194..d99ca134d 100644 --- a/docs/BreastCancer_LIBRA.html +++ b/docs/BreastCancer_LIBRA.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/BreastCancer_breastSegmentation.html b/docs/BreastCancer_breastSegmentation.html index a60c9342a..1bf0a6d8a 100644 --- a/docs/BreastCancer_breastSegmentation.html +++ b/docs/BreastCancer_breastSegmentation.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
@@ -61,7 +61,7 @@
Breast Cancer: Breast Segmentation
-

This application uses LIBRA [1] to extract the breast region in the loaded image.

+

This application uses LIBRA [1] to extract the breast region in the loaded image and is only availabe via the GUI (the Breast Texture Pipeline can be used to generate a mask and perform radiomic analysis via the command line).

REQUIREMENTS:

  • Raw (i.e., "FOR PROCESSING") or vendor post-processed (i.e., "FOR PRESENTATION") FFDM images.
  • FFDM vendors currently supported: GE Healthcare and Hologic.
    • diff --git a/docs/BreastCancer_texture.html b/docs/BreastCancer_texture.html index 1beb8bafe..99093bf85 100644 --- a/docs/BreastCancer_texture.html +++ b/docs/BreastCancer_texture.html @@ -30,7 +30,7 @@
    Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
    diff --git a/docs/CaPTk.TAGFILE b/docs/CaPTk.TAGFILE index 0a84399cc..1e16c18fe 100644 --- a/docs/CaPTk.TAGFILE +++ b/docs/CaPTk.TAGFILE @@ -35,7 +35,7 @@ gs_FAQ_6 gs_FAQ_7 gs_FAQ_8 - gs_FAQ_9 + gs_FAQ_9 How_To_Guides diff --git a/docs/Diffusion_Derivatives.html b/docs/Diffusion_Derivatives.html index 0484cdb03..088da347a 100644 --- a/docs/Diffusion_Derivatives.html +++ b/docs/Diffusion_Derivatives.html @@ -30,7 +30,7 @@
    Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
    diff --git a/docs/Download.html b/docs/Download.html index 19b5ae318..9f693dd1d 100644 --- a/docs/Download.html +++ b/docs/Download.html @@ -30,7 +30,7 @@
    Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
    diff --git a/docs/FAQ.html b/docs/FAQ.html index 81ff184b1..1041290cf 100644 --- a/docs/FAQ.html +++ b/docs/FAQ.html @@ -30,7 +30,7 @@
    Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
    @@ -73,7 +73,7 @@
  • Is there a minimum recommended screen resolution for running CaPTk?
  • Where can I find the CaPTk Docker Image?
  • How do I run the CaPTk Docker Image to show the interface?
    • -
  • What if I am having an issue not listed here?
    • +
  • Is there something wrong with Feature Extraction?

@@ -187,7 +187,10 @@

-u qtuser \ cbica/captk

-What if I am having an issue not listed here?

+Is there something wrong with Feature Extraction? +

Please see the Feature Extraction FAQ.

+

+Is there something wrong with Feature Extraction?

Please open a new issue with us and we will do our best to resolve it.

diff --git a/docs/Getting_Started.html b/docs/Getting_Started.html index ed9a1b92c..720e2d165 100644 --- a/docs/Getting_Started.html +++ b/docs/Getting_Started.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_Atlas.html b/docs/Glioblastoma_Atlas.html index 05751fabe..c9c902380 100644 --- a/docs/Glioblastoma_Atlas.html +++ b/docs/Glioblastoma_Atlas.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_Confetti.html b/docs/Glioblastoma_Confetti.html index 6ce357c45..84ecccd5e 100644 --- a/docs/Glioblastoma_Confetti.html +++ b/docs/Glioblastoma_Confetti.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_Directionality.html b/docs/Glioblastoma_Directionality.html index 255d08b05..c88d1388b 100644 --- a/docs/Glioblastoma_Directionality.html +++ b/docs/Glioblastoma_Directionality.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_EGFRvIII.html b/docs/Glioblastoma_EGFRvIII.html index 607b981bc..ff4c9725f 100644 --- a/docs/Glioblastoma_EGFRvIII.html +++ b/docs/Glioblastoma_EGFRvIII.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_Molecular.html b/docs/Glioblastoma_Molecular.html index ec9c6da7c..c0ba6e68f 100644 --- a/docs/Glioblastoma_Molecular.html +++ b/docs/Glioblastoma_Molecular.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_PHI.html b/docs/Glioblastoma_PHI.html index 6cf68f6be..9058eb70a 100644 --- a/docs/Glioblastoma_PHI.html +++ b/docs/Glioblastoma_PHI.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_Pseudoprogression.html b/docs/Glioblastoma_Pseudoprogression.html index 1757f5f53..f6ff9820c 100644 --- a/docs/Glioblastoma_Pseudoprogression.html +++ b/docs/Glioblastoma_Pseudoprogression.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_Recurrence.html b/docs/Glioblastoma_Recurrence.html index 48e5c0bee..4baee70a6 100644 --- a/docs/Glioblastoma_Recurrence.html +++ b/docs/Glioblastoma_Recurrence.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_Survival.html b/docs/Glioblastoma_Survival.html index a9f6a1cd4..7020403f3 100644 --- a/docs/Glioblastoma_Survival.html +++ b/docs/Glioblastoma_Survival.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Glioblastoma_WhiteStripe.html b/docs/Glioblastoma_WhiteStripe.html index 0fd6b3439..3349ea7fc 100644 --- a/docs/Glioblastoma_WhiteStripe.html +++ b/docs/Glioblastoma_WhiteStripe.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/How_To_Guides.html b/docs/How_To_Guides.html index e1ab509b1..7f5e0d0bf 100644 --- a/docs/How_To_Guides.html +++ b/docs/How_To_Guides.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Installation.html b/docs/Installation.html index 43dd9a963..1b1fb8bc6 100644 --- a/docs/Installation.html +++ b/docs/Installation.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/LungCancer_SBRT.html b/docs/LungCancer_SBRT.html index 032b72f59..e40b74e84 100644 --- a/docs/LungCancer_SBRT.html +++ b/docs/LungCancer_SBRT.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/PCA_Extraction.html b/docs/PCA_Extraction.html index 29c0b2581..a08d946f1 100644 --- a/docs/PCA_Extraction.html +++ b/docs/PCA_Extraction.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/People.html b/docs/People.html index c7f7471db..0489f59fb 100644 --- a/docs/People.html +++ b/docs/People.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Perfusion_Derivatives.html b/docs/Perfusion_Derivatives.html index 51de2b8c7..0f0bc26e8 100644 --- a/docs/Perfusion_Derivatives.html +++ b/docs/Perfusion_Derivatives.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/ReleaseNotes.html b/docs/ReleaseNotes.html index e9308023e..87fe8ab9d 100644 --- a/docs/ReleaseNotes.html +++ b/docs/ReleaseNotes.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Science.html b/docs/Science.html index 10fe6a2c7..a861291be 100644 --- a/docs/Science.html +++ b/docs/Science.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Technical_Reference.html b/docs/Technical_Reference.html index b1fcf9179..e797be37a 100644 --- a/docs/Technical_Reference.html +++ b/docs/Technical_Reference.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/Training_Module.html b/docs/Training_Module.html index 9b673186f..5e8c695e1 100644 --- a/docs/Training_Module.html +++ b/docs/Training_Module.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/ht_FeatureExtraction.html b/docs/ht_FeatureExtraction.html index 1f462c49f..94ce5e98c 100644 --- a/docs/ht_FeatureExtraction.html +++ b/docs/ht_FeatureExtraction.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/ht_Preprocessing.html b/docs/ht_Preprocessing.html index 5fa0282b0..5f43b7058 100644 --- a/docs/ht_Preprocessing.html +++ b/docs/ht_Preprocessing.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/ht_Segmentation.html b/docs/ht_Segmentation.html index 3fc587d79..64f23bf5e 100644 --- a/docs/ht_Segmentation.html +++ b/docs/ht_Segmentation.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/ht_SpecialApps.html b/docs/ht_SpecialApps.html index e8882ed44..22c71e1dc 100644 --- a/docs/ht_SpecialApps.html +++ b/docs/ht_SpecialApps.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
diff --git a/docs/ht_utilities.html b/docs/ht_utilities.html index ab9b6ffcf..a4bc3c2bf 100644 --- a/docs/ht_utilities.html +++ b/docs/ht_utilities.html @@ -30,7 +30,7 @@
Cancer Imaging Phenomics Toolkit (CaPTk) -  1.8.0.Alpha2 +  1.8.0.Alpha3
@@ -73,7 +73,8 @@
  • Test 2 images 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -tb C:/test.nii.gz
  • Create mask from threshold 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -o C:/test.nii.gz -cm 50,1000
  • DICOM to NIfTI conversion 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -o C:/test.nii.gz -d2n
    • -
  • NIfTI to DICOM & DICOM-Seg conversion 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/test_dicom/ -n2d C:/referenceDICOM/
    • +
  • NIfTI to DICOM conversion 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/imageToConvert.nii.gz -o C:/outputDicom/ -n2d C:/referenceDICOM/
    • +
  • NIfTI to DICOM-Seg conversion (using DCMQI) 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/maskToConvert.nii.gz -o C:/outputDicom/ -ds C:/referenceDICOM/ -dsJ C:/dicomSeg.json
    Please see DCMQI's FAQ and use case for JSON-related information.
  • Re-orient image 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output.nii.gz -or RAI
  • Cast image to another pixel type 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -o C:/test_int.nii.gz -c int
  • Thresholding:
    • -
  • Convert file formats 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -o C:/test.mha
    • -
  • Extract Image Series from Joined stack and vice-versa (4D <-> 3D) 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output -j2e 1
+
  • Convert file formats 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -o C:/test.mha -cov
    • 
+
  • Extract Image Series from Joined stack and vice-versa (4D <-> 3D) 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output -j2e 1 # output images are written in the form C:/output_${slice}.nii.gz
+${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output/ -j2e 1 # output images are written in the form C:/output/extractedImage_${slice}.nii.gz
 ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/ -o C:/output.nii.gz -e2j 1.5
    • 
 
  • Transform coordinates from world to image and vice-versa 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -i2w 10,10,30
 ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -w2i 10.5,10.1,30.6
    • 
 
  • Label similarity Metrics between 2 label images: pure mathematical formulations are given as output 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/outputMask.nii.gz -l2s C:/referenceMask.nii.gz
    • 
 
  • BraTS similarity Metrics between 2 label images: special considerations for metrics are done in this mode because output needs to be BraTS-compliant. 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/outputMask.nii.gz -lsb C:/referenceMask.nii.gz
    • 
-
  • Collect information from all images in a directory and put it in CSV 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/inputDirectory -o C:/test/inputDirectoryProperties.csv -co 1 -cF volume -cFE .nii.gz -cP 0,1
    • 
+
  • Collect information from all images in a directory and put it in CSV 
    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/inputDirectory -o C:/test/inputDirectoryProperties.csv \
+-co 1 \ # enable recursion
+-cF volume \ # only process files that contain this string pattern 
+-cFE .nii.gz \ # only process files with this extension 
+-cP 0,1 \ # which properties to read; see usage for all options
    • 
 
 
    For a full list of available applications and examples, please use the command: 
    ${CaPTk_InstallDir}/bin/Utilities -h
 
     
diff --git a/docs/index.html b/docs/index.html
index 2e50b7922..a5e554b14 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/index.qhp b/docs/index.qhp
index 33585a51a..aa80223d4 100644
--- a/docs/index.qhp
+++ b/docs/index.qhp
@@ -5,7 +5,7 @@
   
     doxygen
     
-      
    
+      
    
         
    
           
    
           
    
@@ -46,7 +46,7 @@
         
    
         
    
         
    
-        
    
+        
    
       
    
       
    
         
    
diff --git a/docs/navtreedata.js b/docs/navtreedata.js
index 9e588504e..bd0e0dc0e 100644
--- a/docs/navtreedata.js
+++ b/docs/navtreedata.js
@@ -63,7 +63,7 @@ var NAVTREE =
       [ "Is there a minimum recommended screen resolution for running CaPTk?", "FAQ.html#gs_FAQ_6", null ],
       [ "Where can I find the CaPTk Docker Image?", "FAQ.html#gs_FAQ_7", null ],
       [ "How do I run the CaPTk Docker Image to show the interface?", "FAQ.html#gs_FAQ_8", null ],
-      [ "What if I am having an issue not listed here?", "FAQ.html#gs_FAQ_9", null ]
+      [ "Is there something wrong with Feature Extraction?", "FAQ.html#gs_FAQ_9", null ]
     ] ],
     [ "How To Guides", "How_To_Guides.html", "How_To_Guides" ],
     [ "Scientific Findings using CaPTk", "Science.html", [
diff --git a/docs/pages.html b/docs/pages.html
index d4d1bf5c9..5e1a49b0a 100644
--- a/docs/pages.html
+++ b/docs/pages.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/preprocessing_bias.html b/docs/preprocessing_bias.html
index 198f17c69..285ad26b9 100644
--- a/docs/preprocessing_bias.html
+++ b/docs/preprocessing_bias.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/preprocessing_brats.html b/docs/preprocessing_brats.html
index a85bdbb73..108778245 100644
--- a/docs/preprocessing_brats.html
+++ b/docs/preprocessing_brats.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/preprocessing_dcm2nii.html b/docs/preprocessing_dcm2nii.html
index 7af811d38..2c7d79c88 100644
--- a/docs/preprocessing_dcm2nii.html
+++ b/docs/preprocessing_dcm2nii.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/preprocessing_histoMatch.html b/docs/preprocessing_histoMatch.html
index ecd044d27..d1d1e4f6c 100644
--- a/docs/preprocessing_histoMatch.html
+++ b/docs/preprocessing_histoMatch.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/preprocessing_reg.html b/docs/preprocessing_reg.html
index 3bcb8b3f5..7c3954c35 100644
--- a/docs/preprocessing_reg.html
+++ b/docs/preprocessing_reg.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/preprocessing_susan.html b/docs/preprocessing_susan.html
index c61c7b3f3..4264d7837 100644
--- a/docs/preprocessing_susan.html
+++ b/docs/preprocessing_susan.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/preprocessing_zScoreNorm.html b/docs/preprocessing_zScoreNorm.html
index 97f93a22a..2e44b70da 100644
--- a/docs/preprocessing_zScoreNorm.html
+++ b/docs/preprocessing_zScoreNorm.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/seg_DL.html b/docs/seg_DL.html
index bab468cd8..391fffefe 100644
--- a/docs/seg_DL.html
+++ b/docs/seg_DL.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/seg_GeoTrain.html b/docs/seg_GeoTrain.html
index 134f59fbb..b0c4b360f 100644
--- a/docs/seg_GeoTrain.html
+++ b/docs/seg_GeoTrain.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/seg_Geodesic.html b/docs/seg_Geodesic.html
index d83a67f23..3a43c9009 100644
--- a/docs/seg_Geodesic.html
+++ b/docs/seg_Geodesic.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/seg_SNAP.html b/docs/seg_SNAP.html
index 53c0dd5a7..194fbe1c7 100644
--- a/docs/seg_SNAP.html
+++ b/docs/seg_SNAP.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/tr_FeatureExtraction.html b/docs/tr_FeatureExtraction.html
index 106b40b78..e9462da7d 100644
--- a/docs/tr_FeatureExtraction.html
+++ b/docs/tr_FeatureExtraction.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
diff --git a/docs/tr_integration.html b/docs/tr_integration.html
index 923fe1785..2e748228d 100644
--- a/docs/tr_integration.html
+++ b/docs/tr_integration.html
@@ -30,7 +30,7 @@
  
   
    
    Cancer Imaging Phenomics Toolkit (CaPTk)
-    1.8.0.Alpha2
+    1.8.0.Alpha3
    
    
   
  
@@ -127,12 +127,6 @@ 
    
 
    An example of the list of commands to run to compile CaPTk and its dependencies:
    
 
    git clone https://github.com/CBICA/CaPTk.git
 cd CaPTk
-mkdir bin
-cd bin
-#git lfs fetch --all # downloads all the precompiled binaries for different applications and Qt with the required installation options
-# change ${platform} to either windows, linux or macos (case sensitive)
-wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/${platform}.zip -O precompiledApps.zip 
-wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/${platform}.zip -O qt.zip
 git submodule update --init --recursive # this ensures all submodules are initialized and up-to-date
 mkdir build # this is where we will build all the binaries
 cd build