final commit before merging to master

NEWS

@@ -1,7 +1,7 @@
 ==============
-LESYMAP v0.0.0.9201 (Release date: 2018-09-13)
+LESYMAP v0.0.0.9201 (Release date: 2018-09-14)
 
-  This is a major update, some default outputs have changed:
+  This is a major update, the default SCCAN output has changed:
   - SCCAN weights now show relationship with behavior
   - SCCAN weights can now range -1 to 1
   - added 'directionalSCCAN' argument for back compatbility
@@ -10,6 +10,7 @@ LESYMAP v0.0.0.9201 (Release date: 2018-09-13)
   - removed rawStat argument from SCCAN
   - raw SCCAN weights always returned in rawWeights.img output
   - new outputs returned from SCCAN: eig2 and ccasummary
+  - removed sccan.BehaviorWeight output, info now in eig2 output
   - added sparseness.behav argument to lsm_sccan
   - changed names for lowerSparseness, upperSparseness, nFolds, etc.
   - overall info display improvements

R/lsm_sccan.R

@@ -110,7 +110,7 @@ lsm_sccan <- function(lesmat, behavior, mask, rawStat=F, showInfo=T, optimizeSpa
                       npermsSCCAN=0,
                       smooth=0.4,
                       maxBased=FALSE,
-                      directionalSCCAN=FALSE,
+                      directionalSCCAN=TRUE,
                       ...) {
 
 

README.md

@@ -4,7 +4,7 @@ Lesion to Symptom Mapping (R toolbox)
 *****  
 #### Package details  
 [![Open Source Love](https://badges.frapsoft.com/os/v3/open-source.svg?v=103)](https://github.com/dorianps/LESYMAP)  
-Version:  0.0.0.9009  
+Version:  0.0.0.9201  
 Systems:  Linux, Mac or [Windows Linux Subsystem](https://github.com/stnava/ANTsR/wiki/Installing-ANTsR-in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc).)  
 Language: R (version 3.0 or above)  
 License:  Apache License 2.0  
@@ -39,32 +39,34 @@ library(LESYMAP)
 example(lesymap)
 ```
 ```
-18:34:35 Running LESYMAP 0.0.0.9001   
-18:34:35 Checking a few things...  
-18:34:35 Loading behavioral data...131 scores found.  
-18:34:35 Computing mask from average >= 10% ...  
-18:35:23 Computing unique patches...  
-18:36:01 Found 195102 patches in 326828 voxels - 1.7 times more voxels  
-18:36:01 Using existing lesion matrix... 131x195102  
-18:36:01 Running analysis: BMfast ...  
-18:36:04 Correcting p-values: fdr ...  
-18:36:04 Preparing images...  
-18:36:05 Logging call details...  
-18:36:05 Done! 1.5 mins   
+3:46:03 Running LESYMAP 0.0.0.9201 
+13:46:03 Checking a few things...
+13:46:03 Loading behavioral data...131 scores found.
+13:46:03 Filenames as input, checking lesion values on 1st image...
+13:46:04 Searching voxels lesioned >= 10% subjects...326828 found
+13:46:36 Computing unique patches...
+13:46:55 Found 195102 patches in 326828 voxels - 1.7 times more voxels
+13:46:55 Using existing lesion matrix... 131x195102
+13:46:55 Running analysis: BMfast ...
+13:46:57 Correcting p-values: fdr ...
+13:46:57 Preparing images...
+13:46:57 Logging call details...
+13:46:57 Done! 54.1 secs 
 Hit <Return> to see next plot: 
 ```
 Check out how this example looks on [the screen](https://youtu.be/0WQXEgip_zk).  
 
 *****    
 ## Documentation
+***[New]*** [What's new in v0.0.0.9201](https://github.com/dorianps/LESYMAP/wiki/What's-new-in-v0.0.0.9201)  
 [What is lesion to symptom mapping](https://github.com/dorianps/LESYMAP/wiki/What-is-lesion-to-symptom-mapping)  
 [Installing LESYMAP](https://github.com/dorianps/LESYMAP/wiki/Lesymap-Installation)  
 [Registering lesions in template space](https://github.com/dorianps/LESYMAP/wiki/Registering-lesions-in-template-space)  
 [Provided data](https://github.com/dorianps/LESYMAP/wiki/Data)  
 [Understanding permutations](https://github.com/dorianps/LESYMAP/wiki/Understanding-permutations)  
 [Fast lesion drawing in ITKsnap](https://www.youtube.com/watch?v=ZVmINdWk5R4)  
 [All Videos](https://github.com/dorianps/LESYMAP/wiki/Videos)  
-***[New]*** [SCCAN questions](https://github.com/dorianps/LESYMAP/wiki/SCCAN-questions)  
+[SCCAN questions](https://github.com/dorianps/LESYMAP/wiki/SCCAN-questions)  
 [Known limitations](https://github.com/dorianps/LESYMAP/wiki/Known-Limitations)
 
 *****