new version (v1.0.20190902)

README.md

@@ -2,77 +2,37 @@
 
 ##### 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
+MRIcron is a viewer for brain imaging data. 
 
- - The latest stable version is released at [NITRC](https://www.nitrc.org/projects/mricron)
+##### Installing
 
-##### Recent Versions
+You can download the software from several locations:
 
-20-December-2017 (v1.0.20171220)
- - Now includes [dcm2niix](https://github.com/rordenlab/dcm2niix) (import menu).
- - NPM and dcm2nii no longer included (as they were deprecated)
-
-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).
+ - Download the latest version from [NITRC](https://www.nitrc.org/projects/mricron).
+ - Download the [Github](https://github.com/neurolabusc/MRIcroGL/releases).
+ - Run the following command to get the latest version for Linux, Macintosh or Windows: 
+   * `curl -fLO https://github.com/rordenlab/MRIcroGL12/releases/latest/download/MRIcroGL_linux.zip`
+   * `curl -fLO https://github.com/rordenlab/MRIcroGL12/releases/latest/download/MRIcroGL_macOS.dmg`
+   * `curl -fLO https://github.com/rordenlab/MRIcroGL12/releases/latest/download/MRIcroGL_windows.zip`
+
+Once you have downloaded and extracted the software, you may want to visit the [wiki](https://www.nitrc.org/plugins/mwiki/index.php/mricron:MainPage) for usage advice.
 
 ##### License
 
 This software includes a [BSD license](https://opensource.org/licenses/BSD-2-Clause)
 
-##### Compiling your own software
+##### Future
 
-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/
+MRIcron is robust and stable, but development efforts have moved to MRIcroGL. The latest releases of MRIcron only include the MRIcron viewer and the dcm2niix image converter. Once upon a time, the software was distributed with statistics (NPM) and legacy image converter (dcm2nii). One can still download old releases of MRIcron from [NITRC](https://www.nitrc.org/projects/mricron) or compile these legacy tools (see next section).
 
-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:
-     -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:
-      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
+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.
 
-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 -
-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
+ - MRIcron development has moved to [MRIcroGL](https://github.com/rordenlab/MRIcroGL12/releases)
+ - NPM development has been moved to [NiiStat](https://github.com/neurolabusc/NiiStat)
+ - dcm2nii development has been moved to [dcm2niix](https://github.com/neurolabusc/dcm2niix)
 
--------------------------------------------
-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
+##### Compiling your own software
 
--------------------------------------------
-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]"
-   Linking tab: make sure the "Pass options to linker" checkbox is UNCHECKED.
-3.) Choose Run/Run to build and execute the program
+You can build MRIcron using [Lazarus](https://www.lazarus-ide.org).
+ - Launch Lazarus and open the project.
+ - Choose Run/Run to build and execute the program

_lazwin.bat

@@ -15,11 +15,11 @@ copy /Y mricron.exe d:\neuro\mricron
 call _clean.bat
 del d:\neuro\MRIcron\mricron.ini
 REM compress MRIcron
-c:\Progra~1\7-Zip\7z a -tzip d:\neuro\MRIcron_Windows.zip d:\neuro\MRIcron
+c:\Progra~1\7-Zip\7z a -tzip d:\neuro\MRIcron_windows.zip d:\neuro\MRIcron
 REM copy /Y c:\pas\wincron.zip Y:\mcbi\MCBI\CRNL\sw\mricron\win.zip
 
 REM compress Source
-# c:\Progra~1\7-Zip\7z a -tzip c:\pas\mricron_windows.zip c:\pas\mricron 
+# c:\Progra~1\7-Zip\7z a -tzip c:\pas\mricron_windows_src.zip c:\pas\mricron 
 REM copy c:\pas\srccron.zip Y:\mcbi\MCBI\CRNL\sw\mricron\source.zip
 
 

_osx.command

@@ -12,7 +12,10 @@
 	cp dcm2niix /Users/rorden/Documents/mricron/MRIcron/MRIcron.app/Contents/Resources/dcm2niix
 SKIPDCM2NIIX
 
-cd /Users/rorden/Documents/pas/mricron
+cp /usr/local/bin/dcm2niix /Users/chris/Neuro/MRIcron/MRIcron.app/Contents/Resources/dcm2niix
+
+
+cd /Users/chris/src/MRIcron
 
 chmod 777 ./_xclean.bat
 ./_xclean.bat
@@ -48,11 +51,11 @@ SKIPNPM
 #Current FPC 3.0.0 can not compile on OSX 10.11 El Capitan, so use 3.1.1
 #/Users/rorden/lazarus/lazbuild ./mricron.lpr --cpu=x86_64 --ws=cocoa --compiler="/usr/local/lib/fpc/3.1.1/ppcx64"
 
-/Users/rorden/lazarus/lazbuild ./mricron.lpr --cpu=x86_64 --ws=cocoa
+/Users/chris/src/lazarus/lazbuild ./mricron.lpr --cpu=x86_64 --ws=cocoa
 
 strip ./mricron
 
-cp ./mricron /Users/rorden/Documents/mricron/MRIcron/MRIcron.app/Contents/MacOS/MRIcron
+cp ./mricron /Users/chris/Neuro/MRIcron/MRIcron.app/Contents/MacOS/MRIcron
 
 awk '{gsub(/Active="MacOS"/,"Active=\"Default\"");}1' mricron.lps > mricron.tmp && mv mricron.tmp mricron.lps
 
@@ -61,11 +64,10 @@ awk '{gsub(/Active="MacOS"/,"Active=\"Default\"");}1' mricron.lps > mricron.tmp
 rm -rf lib
 rm -rf backup
 
-cd /Users/rorden/Documents/pas/
-zip -r /Users/rorden/Documents/mricron_source.zip mricron
-
-cd /Users/rorden/Documents/
-zip -r /Users/rorden/Documents/mricron_osx.zip mricron
-
+cd /Users/chris/src
+zip -r /Users/chris/src/mricron_source.zip mricron
 
+cd /Users/chris/Neuro
+hdiutil create -volname MRIcron -srcfolder /Users/chris/Neuro/MRIcron -ov -format UDZO -layout SPUD -fs HFS+J  mricron_macOS.dmg
+codesign -s "Developer ID Application: Christopher Rorden" mricron_macOS.dmg
 

_xclean.bat

@@ -1,6 +1,9 @@
 #!/bin/sh
 
 find . -name \*.dcu -type f -delete
+rm -rf lib
+rm -rf backup
+rm  -r .DS_Store
 rm  -r *.a
 rm  -r *.o
 rm  -r *.ppu
@@ -27,6 +30,7 @@ rm  -r *.o
 rm  -r *.ppu
 rm -r *.bak
 cd ..
+rm -rf ./common/backup
 
 
 cd ./dcm2nii

batch.pas

@@ -126,11 +126,11 @@ procedure BatchVOI;
         ImgForm.UpdateLayerMenu;
         lBGStrings := TStringList.Create;
         if (ssShift in KeyDataToShiftState(vk_Shift)) then begin
-                GetFilesInDir(ExtractFileDir(HdrForm.OpenHdrDlg.Filename),lBGStrings)
+                GetFilesInDir(ExtractFileDir(ImgForm.OpenHdrDlg.Filename),lBGStrings)
         end else begin
-            if not OpenDialogExecute(kImgFilter,'Select background images (stat maps)',true) then
+            if not ImgForm.OpenDialogExecute(kImgFilter,'Select background images (stat maps)',true) then
                exit;
-            lBGStrings.AddStrings(HdrForm.OpenHdrDlg.Files);
+            lBGStrings.AddStrings(ImgForm.OpenHdrDlg.Files);
         end;
         lNumberofP:= lBGStrings.Count;
         if  lNumberofP < 1 then begin
@@ -139,8 +139,8 @@ procedure BatchVOI;
 
         end;
 
-	if not OpenDialogExecute(kImgFilter,'Select overlay images (ROIs)',true) then exit;
-	lNumberofFiles:= HdrForm.OpenHdrDlg.Files.Count;
+	if not ImgForm.OpenDialogExecute(kImgFilter,'Select overlay images (ROIs)',true) then exit;
+	lNumberofFiles:= ImgForm.OpenHdrDlg.Files.Count;
         if  lNumberofFiles < 1 then
 		exit;
     TextForm.MemoT.Lines.Clear;
@@ -165,11 +165,11 @@ procedure BatchVOI;
                  lStr := 'max10pct'
             else
                 lStr := 'mean';
-            lStr := lStr +kTextSep+ (HdrForm.OpenHdrDlg.Files[lInc-1]);
+            lStr := lStr +kTextSep+ (ImgForm.OpenHdrDlg.Files[lInc-1]);
             for lP := 1 to lNumberofP do begin
                 lFilename := lBGStrings.Strings[lP-1];
                 ImgForm.OpenAndDisplayImg(lFilename,True);
-                lFilename := HdrForm.OpenHdrDlg.Files[lInc-1];
+                lFilename := ImgForm.OpenHdrDlg.Files[lInc-1];
 	              ImgForm.OverlayOpenCore ( lFilename, 2);
                 if lP = 1 then
                    lStr := lStr + kTextSep+ inttostr(VOIVol(2) );