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neurolabusc · Oct 6, 2016 · 26cb1e3 · 26cb1e3
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diff --git a/Readme.txt → README.md b/Readme.txt → README.md
@@ -1,48 +1,72 @@
+# MRIcron / NPM / dcm2nii
+
+##### About
+
+MRIcron is a viewer for brain imaging data. NPM is a tool for non parametric analysis of neuroimaging lesion data. dcm2nii is designed for converting the complicated DICOM format used in medical imaging to the simple NIfTI format preferred by scientists. These tools are mature and hopefully robust but no longer in active development.
+ - MRIcron development has moved to [MRIcroGL](https://github.com/neurolabusc/MRIcroGL)
+ - NPM development has been moved to [NiiStat](https://github.com/neurolabusc/NiiStat)
+ - dcm2nii development has been moved to [dcm2niix](https://github.com/neurolabusc/dcm2niix)
+
+ ##### Downloading compiled software
+
+ - The latest stable version is released at [NITRC](https://www.nitrc.org/projects/mricron)
+
+ ##### Recent Versions
+
+2-May-2016
+ - MRIcron : Improved ability to copy images to clipboard
+ - NPM : Permutation thresholds in previous versions were not completely random, while the influence of this was typically negligible when images were listed in random order, this could make the thresholds slightly more liberal or conservative if the images listed in a sorted manner (e.g. lesion size, behavioral deficit). This new version revamps the randomization process, including using the [random number generator described by Marsaglia Zaman](http://paulbourke.net/miscellaneous/random/). Permutation thresholds are now more robust, albeit slower. THe enhanced 64-bit version allows the user to select more threads, which can accelerate the software (assuming your computer has more CPUs).
+
+##### License
+
+This software includes a [BSD license](https://opensource.org/licenses/BSD-2-Clause)
+
+##### Compiling your own software
+
 This is a beta release of MRIcron. You can compile this using Lazarus. It has been compiled on Windows, Linux-x86, OSX-x86 and OSX-PPC. It requires builds of Lazarus and FreePascal created after October 7, 2007.
  http://www.hu.freepascal.org/lazarus/
 
--------------------------------------------
-To compile for OSX [Carbon] - 
+To compile for OSX [Carbon] -
 1.) Launch Lazarus and open the project.
 2.) Select Project/CompilerOptions
    Paths tab: make sure the "LCL widget type" is set to "carbon"
    Linking tab: make sure the "Pass options to linker" checkbox is selected and
       set the text to "-framework carbon" (no quotes).
 3.) Select Project/ProjectOptions and set "Use application bundle for running and debugging"
-4.) If using OSX 10.5 or later, add to Project / Compiler options / Other / Custom options:    
+4.) If using OSX 10.5 or later, add to Project / Compiler options / Other / Custom options:
      -k-macosx_version_min -k10.4
      -XR/Developer/SDKs/MacOSX10.4u.sdk/
      Alternative: Project/ProjectOptions/Linking/ Check 'pass options to linker' and add this line -macosx_version_min 10.4
 5.) For debugging, you will want to create an alias from the application folder to the compiled executable:
-   The exact value will depend on your paths, but it will be similar to this: 
+   The exact value will depend on your paths, but it will be similar to this:
       rm ~/Documents/mricron/mricron.app/mricron
       ln -s ~/Documents/mricron/mricron ~/Documents/mricron/mricron.app/mricron
       rm ~/Documents/mricron/npm/npm.app/npm
       ln -s ~/Documents/mricron/npm/npm ~/Documents/mricron/npm/npm.app/npm
       rm ~/Documents/mricron/dcm2nii/dcm2niigui.app/dcm2niigui
       ln -s ~/Documents/mricron/dcm2nii/dcm2niigui ~/Documents/mricron/dcm2nii/dcm2niigui.app/dcm2niigui
-    
+
 6.) Select Run/Run to build and execute your program
 7.) For making an executable to distribute, control+click on the program's .app folder (e.g. the file named mricron that has a brain icon) and choose "show package contents" - move the executable generated with Lazarus into the folder, overwriting the symbolic link created in step 4.
 
 -------------------------------------------
-To compile for Linux GTK1 - 
+To compile for Linux GTK1 -
 1.) Launch Lazarus and open the project.
 2.) Select Project/CompilerOptions
    Paths tab: make sure the "LCL widget type" is set to "default [gtk]"
    Linking tab: make sure the "Pass options to linker" checkbox is UNCHECKED.
 3.) Choose Run/Run to build and execute the program
 
 -------------------------------------------
-To compile for Linux GTK2 - 
+To compile for Linux GTK2 -
 1.) Launch Lazarus and open the project.
 2.) Select Project/CompilerOptions
    Paths tab: make sure the "LCL widget type" is set to "gtk2"
    Linking tab: make sure the "Pass options to linker" checkbox is UNCHECKED.
 3.) Choose Run/Run to build and execute the program
 
 -------------------------------------------
-To compile for Windows - 
+To compile for Windows -
 1.) Launch Lazarus and open the project.
 2.) Select Project/CompilerOptions
    Paths tab: make sure the "LCL widget type" is set to "default [Win API]"

diff --git a/common/cpucount.pas b/common/cpucount.pas
@@ -49,7 +49,6 @@ function GetLogicalCpuCount: Integer;
 end;
 
 {$ELSE} //If UNIX ELSE NOT Unix -> windows
-end;
 
 uses Windows;
 function GetLogicalCpuCount: Integer;

diff --git a/npm/LesionStatThds.pas b/npm/LesionStatThds.pas
@@ -652,7 +652,6 @@ procedure TLesionContinuous.Analyze (lttest,lBM: boolean; lnCrit,lnPermute,lThre
                  lOutImgT^[lPos2Offset] := lT;
                  lPrevZValsT[lPatternPos] := lT;
               end;
-
               if lBM then begin
                       tBM3 (lnControlsPlusLesion, lLesionOrderp, lSymptomRA,lBMz,lDF, lnGroup0);
                       //if lBMz > 55 then

diff --git a/npm/npm.lpi b/npm/npm.lpi
@@ -47,8 +47,8 @@
         <HasResources Value="True"/>
         <ResourceBaseClass Value="Form"/>
         <EditorIndex Value="1"/>
-        <TopLine Value="1131"/>
-        <CursorPos X="63" Y="1140"/>
+        <TopLine Value="1108"/>
+        <CursorPos X="25" Y="1109"/>
         <UsageCount Value="208"/>
         <Loaded Value="True"/>
         <LoadedDesigner Value="True"/>
@@ -202,10 +202,9 @@
       </Unit20>
       <Unit21>
         <Filename Value="LesionStatThds.pas"/>
-        <IsVisibleTab Value="True"/>
         <EditorIndex Value="9"/>
         <TopLine Value="629"/>
-        <CursorPos X="27" Y="630"/>
+        <CursorPos X="40" Y="633"/>
         <UsageCount Value="68"/>
         <Loaded Value="True"/>
       </Unit21>
@@ -290,9 +289,10 @@
       </Unit34>
       <Unit35>
         <Filename Value="unpm.pas"/>
+        <IsVisibleTab Value="True"/>
         <EditorIndex Value="4"/>
-        <TopLine Value="1173"/>
-        <CursorPos X="18" Y="1173"/>
+        <TopLine Value="92"/>
+        <CursorPos X="155" Y="111"/>
         <UsageCount Value="92"/>
         <Loaded Value="True"/>
       </Unit35>
@@ -347,123 +347,123 @@
     </Units>
     <JumpHistory Count="30" HistoryIndex="29">
       <Position1>
-        <Filename Value="turbolesion.pas"/>
-        <Caret Line="484" Column="47" TopLine="480"/>
+        <Filename Value="brunner.pas"/>
+        <Caret Line="639" Column="20" TopLine="609"/>
       </Position1>
       <Position2>
-        <Filename Value="turbolesion.pas"/>
-        <Caret Line="369" Column="20" TopLine="346"/>
+        <Filename Value="LesionStatThds.pas"/>
+        <Caret Line="690" Column="17" TopLine="661"/>
       </Position2>
       <Position3>
         <Filename Value="brunner.pas"/>
-        <Caret Line="18" Column="24"/>
+        <Caret Line="32" Column="20" TopLine="23"/>
       </Position3>
       <Position4>
-        <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="542" Column="53" TopLine="532"/>
+        <Filename Value="brunner.pas"/>
+        <Caret Line="670" Column="32" TopLine="651"/>
       </Position4>
       <Position5>
-        <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="546" Column="14" TopLine="531"/>
+        <Filename Value="brunner.pas"/>
+        <Caret Line="19" Column="32"/>
       </Position5>
       <Position6>
-        <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="557" Column="29" TopLine="538"/>
+        <Filename Value="brunner.pas"/>
+        <Caret Line="20" Column="27"/>
       </Position6>
       <Position7>
         <Filename Value="brunner.pas"/>
-        <Caret Line="639" Column="20" TopLine="609"/>
+        <Caret Line="21" Column="28"/>
       </Position7>
       <Position8>
-        <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="690" Column="17" TopLine="661"/>
+        <Filename Value="brunner.pas"/>
+        <Caret Line="89" Column="29" TopLine="57"/>
       </Position8>
       <Position9>
         <Filename Value="brunner.pas"/>
-        <Caret Line="32" Column="20" TopLine="23"/>
+        <Caret Line="668" Column="31" TopLine="636"/>
       </Position9>
       <Position10>
         <Filename Value="brunner.pas"/>
-        <Caret Line="670" Column="32" TopLine="651"/>
+        <Caret Line="22" Column="28"/>
       </Position10>
       <Position11>
         <Filename Value="brunner.pas"/>
-        <Caret Line="19" Column="32"/>
+        <Caret Line="101" Column="28" TopLine="69"/>
       </Position11>
       <Position12>
         <Filename Value="brunner.pas"/>
-        <Caret Line="20" Column="27"/>
+        <Caret Line="110" Column="31" TopLine="79"/>
       </Position12>
       <Position13>
         <Filename Value="brunner.pas"/>
-        <Caret Line="21" Column="28"/>
+        <Caret Line="126" Column="26" TopLine="95"/>
       </Position13>
       <Position14>
         <Filename Value="brunner.pas"/>
-        <Caret Line="89" Column="29" TopLine="57"/>
+        <Caret Line="127" Column="26" TopLine="96"/>
       </Position14>
       <Position15>
         <Filename Value="brunner.pas"/>
-        <Caret Line="668" Column="31" TopLine="636"/>
+        <Caret Line="140" Column="44" TopLine="109"/>
       </Position15>
       <Position16>
         <Filename Value="brunner.pas"/>
-        <Caret Line="22" Column="28"/>
+        <Caret Column="35"/>
       </Position16>
       <Position17>
         <Filename Value="brunner.pas"/>
-        <Caret Line="101" Column="28" TopLine="69"/>
+        <Caret Line="14" Column="15"/>
       </Position17>
       <Position18>
-        <Filename Value="brunner.pas"/>
-        <Caret Line="110" Column="31" TopLine="79"/>
+        <Filename Value="LesionStatThds.pas"/>
+        <Caret Line="47" Column="68" TopLine="42"/>
       </Position18>
       <Position19>
-        <Filename Value="brunner.pas"/>
-        <Caret Line="126" Column="26" TopLine="95"/>
+        <Filename Value="LesionStatThds.pas"/>
+        <Caret Line="724" Column="48" TopLine="694"/>
       </Position19>
       <Position20>
-        <Filename Value="brunner.pas"/>
-        <Caret Line="127" Column="26" TopLine="96"/>
+        <Filename Value="LesionStatThds.pas"/>
+        <Caret Line="542" Column="16" TopLine="524"/>
       </Position20>
       <Position21>
-        <Filename Value="brunner.pas"/>
-        <Caret Line="140" Column="44" TopLine="109"/>
+        <Filename Value="LesionStatThds.pas"/>
+        <Caret Line="632" Column="50" TopLine="630"/>
       </Position21>
       <Position22>
-        <Filename Value="brunner.pas"/>
-        <Caret Column="35"/>
+        <Filename Value="LesionStatThds.pas"/>
       </Position22>
       <Position23>
-        <Filename Value="brunner.pas"/>
-        <Caret Line="14" Column="15"/>
+        <Filename Value="LesionStatThds.pas"/>
+        <Caret Line="3" Column="126"/>
       </Position23>
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         <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="47" Column="68" TopLine="42"/>
+        <Caret Line="562" Column="7" TopLine="528"/>
       </Position24>
       <Position25>
-        <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="724" Column="48" TopLine="694"/>
+        <Filename Value="npmform.pas"/>
+        <Caret Line="1133" Column="13" TopLine="1131"/>
       </Position25>
       <Position26>
-        <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="542" Column="16" TopLine="524"/>
+        <Filename Value="npmform.pas"/>
+        <Caret Line="1140" Column="35" TopLine="1131"/>
       </Position26>
       <Position27>
-        <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="632" Column="50" TopLine="630"/>
+        <Filename Value="npmform.pas"/>
+        <Caret Line="377" Column="34" TopLine="358"/>
       </Position27>
       <Position28>
-        <Filename Value="LesionStatThds.pas"/>
+        <Filename Value="npmform.pas"/>
+        <Caret Line="1140" Column="35" TopLine="1108"/>
       </Position28>
       <Position29>
-        <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="3" Column="126"/>
+        <Filename Value="npmform.pas"/>
+        <Caret Line="377" Column="34" TopLine="358"/>
       </Position29>
       <Position30>
-        <Filename Value="LesionStatThds.pas"/>
-        <Caret Line="562" Column="7" TopLine="528"/>
+        <Filename Value="unpm.pas"/>
+        <Caret Line="1173" Column="3" TopLine="1173"/>
       </Position30>
     </JumpHistory>
   </ProjectOptions>

diff --git a/npm/npmform.lfm b/npm/npmform.lfm
@@ -2,11 +2,11 @@ object MainForm: TMainForm
   Left = 468
   Height = 418
   Top = 213
-  Width = 542
+  Width = 640
   ActiveControl = Memo1
   Caption = 'Non-Parametric Mapping'
   ClientHeight = 418
-  ClientWidth = 542
+  ClientWidth = 640
   Menu = MainMenu1
   OnClose = FormClose
   OnCreate = FormCreate
@@ -17,25 +17,26 @@ object MainForm: TMainForm
     Left = 0
     Height = 393
     Top = 0
-    Width = 542
+    Width = 640
     Align = alClient
     ScrollBars = ssAutoBoth
     TabOrder = 0
+    WordWrap = False
   end
   object Panel1: TPanel
     Left = 0
     Height = 25
     Top = 393
-    Width = 542
+    Width = 640
     Align = alBottom
     ClientHeight = 25
-    ClientWidth = 542
+    ClientWidth = 640
     TabOrder = 1
     object ProgressBar1: TProgressBar
       Left = 1
       Height = 23
       Top = 1
-      Width = 540
+      Width = 638
       Align = alClient
       TabOrder = 0
     end
-Original file line number
+Diff line change
@@ Expand Up / @@ -49,7 +49,6 @@ function GetLogicalCpuCount: Integer; @@
     end;
     {$ELSE} //If UNIX ELSE NOT Unix -> windows
-    end;
     uses Windows;
     function GetLogicalCpuCount: Integer;
@@ Expand Down @@