Initial Commit

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+.DS_Store

README.md

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+## About
+
+i2nii converts several scientific and medical imaging formats to the popular [NIfTI](https://nifti.nimh.nih.gov/nifti-1) format. NIfTI is used by many neuroimaging tools including FSL, SPM, and AFNI. Note that this tool will not convert images from DICOM format, though the companion [dcm2niix](https://github.com/rordenlab/dcm2niix) will. Likewise, it will not convert TIFF or many microscopy formats, though the [Bio-Formats module](https://docs.openmicroscopy.org/bio-formats/5.9.2/supported-formats.html) of [ImageJ/Fiji](https://fiji.sc) can convert these.
+
+i2nii shares the image reading functions of the [MRIcroGL](https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage) viewer. If you prefer a drag-and-drop graphical user interface, you should use MRIcroGL. In contrast, i2nii is designed to be used from the command line. Compiled excutables are provided for Linux, MacOS and Windows. The source code should compile on a [wide range](https://www.freepascal.org/download.html) of operating systems. 
+
+## Installation
+
+You can get i2nii using two methods:
+
+ - (Recommended) Download latest compiled release from [Github](https://github.com/rordenlab/i2nii/releases).
+ - (Developers) Download the source code from [GitHub](https://github.com/rordenlab/i2nii).
+
+## Usage
+
+
+```
+Chris Rorden's i2nii v1.0.20190909
+usage: i2nii [options] <in_file(s)>
+ Options :
+ -z : gz compress images (y/n, default n)
+ -h : show help
+ -o : output directory (omit to save to input folder)
+ Examples :
+  i2nii -z y ecat.v
+  i2nii img1.pic img2.pic
+  i2nii -o ~/out "spaces in name.bvox"
+  i2nii ./test/sivic.idf
+  i2nii -o "~/my out" "input.nrrd"
+```  
+
+## Limitations
+
+This software is provided as is. There are clear limitations.
+
+ - Many of the file formats are poorly documented. In partifular with respect to spatial scale and orientation. Some of these problems are inherent to the format (e.g. [Blender Voxel data](http://pythology.blogspot.com/2014/08/you-can-do-cool-stuff-with-manual.html) contains no spatial information at all). In other cases, this software could be improved to better handle these formats. It is open source, so feel free to contribute. However, due to these limitations, one should take care using this software.
+ - The NIfTI format is explicitly designed to store spatial images. Some supported formats handle a much wider range of data. For example, Interfile can encode both raw PET data as well as reconstructed PET spatial images. The NIfTI format is not well suited for the former, though it can cope with the latter.
+
+## Compiling
+
+It is generally recommended that download a pre-compiled executable (see previous section). However, you can compile your own copy from source code.
+
+ - Download and install [FreePascal for your operating system](https://www.freepascal.org/download.html). For Debian-based unix this may be as easy as `sudo apt-get install fp-compiler`. For other operating systems, you may simply want to install FreePascal from the latest [Lazarus distribution](https://sourceforge.net/projects/lazarus/files/).
+ - From the terminal, go inside the directory with the source files and run the following commands to build and test your compilation:
+   * fpc i2nii
+   * ./i2nii -o ./test/sivic.idf
+
+
+## Supported Image Formats
+
+i2nii should automatically detect and convert the following image formats. Be aware that not all these formats have spatial transformations. Further, support for all features of these formats may be incomplete.
+
+ - [AFNI Brik](https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.attributes.html)(.head).
+ - [Analyze](http://imaging.mrc-cbu.cam.ac.uk/imaging/FormatAnalyze)(.hdr).
+ - [Bio-Rad PIC](https://docs.openmicroscopy.org/bio-formats/5.8.2/formats/bio-rad-pic.html)(.pic).
+ - [Blender Voxel data](http://pythology.blogspot.com/2014/08/you-can-do-cool-stuff-with-manual.html)(.bvox).
+ - [BrainVoyager VMR](https://support.brainvoyager.com/brainvoyager/automation-development/84-file-formats/343-developer-guide-2-6-the-format-of-vmr-files)(.vmr, .v16).
+ - [DeltaVision](https://docs.openmicroscopy.org/bio-formats/5.8.2/formats/deltavision.html)(.dv).
+ - [DICOM](http://people.cas.sc.edu/rorden/dicom/index.html)(varies).
+ - [ECAT](http://nipy.org/nibabel/reference/nibabel.ecat.html)(.v).
+ - [FreeSurfer MGH/MGZ Volume](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat)(.mgh/.mgz).
+ - [Guys Image Processing Lab](http://rview.colin-studholme.net/rview/rv9manual/fileform.html#GIPL)(.gipl).
+ - [ICS Image Cytometry Standard](https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.990110502)(.ics).
+ - [INterfile](https://www.ncbi.nlm.nih.gov/pubmed/2616095)(.varies, limited support).
+ - [ITK MHA/MHD](https://itk.org/Wiki/MetaIO/Documentation)(.mha/.mhd).
+ - [Leica TIFF](https://en.wikipedia.org/wiki/TIFF)(.lsm).
+ - [MRTrix Volume](https://mrtrix.readthedocs.io/en/latest/getting_started/image_data.html)(.mif/.mih; not all variants supported).
+ - [NIfTI](https://brainder.org/2012/09/23/the-nifti-file-format/)(.hdr/.nii/.nii.gz/.voi).
+ - [NRRD](http://teem.sourceforge.net/nrrd/format.html)(.nhdr/.nrrd).
+ - [POV-Ray Density_File](https://www.povray.org/documentation/view/3.6.1/374/)(.df3).
+ - [TIFF](https://en.wikipedia.org/wiki/TIFF)(.tif/.tiff/varies).
+ - [Spectroscopic Imaging, VIsualization and Computing (SIVIC)](https://radiology.ucsf.edu/research/labs/nelson#accordion-software)(.idf).
+ - [Stimulate Sdt](https://www.cmrr.umn.edu/stimulate/stimUsersGuide/node57.html)(.spr/.sdt)
+ - [Vaa3D](https://github.com/Vaa3D)(.v3draw).
+ - [VTK Legacy Voxel Format](https://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf)(.vtk).
+
+If your image format is not supported directly by MRIcroGL, you may want to see if it is supported by the [Bio-Formats module](https://docs.openmicroscopy.org/bio-formats/5.9.2/supported-formats.html) of [ImageJ/Fiji](https://fiji.sc). If so, you can open the image with the module and save it as NIfTI or NRRD to read it with MRIcroGL.
+

_clean.command

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+#!/bin/sh
+# change to working directory to location of command file: http://hints.macworld.com/article.php?story=20041217111834902
+here="`dirname \"$0\"`"
+cd "$here" || exit 1
+rm -rf *.o
+rm -rf *.ppu
+rm -rf *.nii
+rm -rf lib
+rm -rf backup
+strip i2nii

dialogsx.pas

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+unit dialogsx;
+{$mode Delphi} //{$mode objfpc}
+{$Include isgui.inc}
+{$H+}
+interface
+uses
+
+SysUtils,IniFiles;   
+
+{$IFNDEF GUI}
+type
+  TMsgDlgBtn = (mbYes, mbNo, mbOK, mbCancel, mbAbort, mbRetry, mbIgnore, mbAll, mbNoToAll, mbYesToAll, mbHelp);
+  TMsgDlgButtons = set of TMsgDlgBtn;
+  TMsgDlgType = (mtWarning, mtError, mtInformation, mtConfirmation, mtCustom);
+{$ENDIF}
+procedure Msg (lStr: string);
+procedure ShowMsg (lStr: string);
+procedure msgfx (a,b,c,d: double); overload; //fx used to help debugging - reports number values
+//function MsgDlg(const Msg: string; DlgType: TMsgDlgType; Buttons: TMsgDlgButtons; HelpCtx: Longint): Word;
+function GetInt(lStr: string; lMin,lDefault,lMax: integer): integer;
+function GetFloat(lStr: string; lMin,lDefault,lMax: single): single;
+procedure MyReadLn;//no GUI: waits for user
+function GetStr(lPrompt: string): string;
+//procedure vx (a,b,c,d: double); 
+
+const
+ mrCancel = 2;
+ mrAbort = 1;//	idAbort
+ mrNo = 0;
+implementation
+{$IFDEF GUI}uses
+  dialogs; {$ENDIF}
+
+procedure vx (a,b,c,d: double);  //vx used to help debugging - reports number values
+begin
+	msg(floattostr(a)+':'+floattostr(b)+':'+floattostr(c)+':'+floattostr(d));
+end;
+
+
+procedure MyReadLn;
+{$IFDEF GUI}
+begin
+  //do nothing
+end;
+{$ELSE}
+begin
+  {$IFNDEF UNIX}
+ if IsConsole then
+		ReadLn;
+   {$ENDIF}
+end;
+{$ENDIF}
+
+function MsgDlg(const Msg: string; DlgType: TMsgDlgType; Buttons: TMsgDlgButtons; HelpCtx: Longint): Word;
+{$IFDEF GUI}
+begin
+  result := 0;
+  ShowMsg('WARNING: MsgDlg not coded. Unabled to process this '+Msg);
+{$ELSE}
+begin
+  result := 0;
+  writeln('WARNING: dialogs not being used. Unabled to process this '+Msg);
+{$ENDIF}
+end;
+
+procedure ShowMsg (lStr: string);
+begin
+{$IFDEF GUI}
+         ShowMessage(lStr);  //if you get an error here - adjust isgui.inc
+{$ELSE}
+        writeln(lStr)
+{$ENDIF}
+end;
+procedure msgfx (a,b,c,d: double); overload; //fx used to help debugging - reports number values
+begin
+    {$IFDEF GUI}
+	msg(floattostr(a)+'x'+floattostr(b)+'x'+floattostr(c)+'x'+floattostr(d));
+    {$ELSE}
+	msg(floattostr(a)+'x'+floattostr(b)+'x'+floattostr(c)+'x'+floattostr(d));
+    {$ENDIF}
+end;
+
+procedure Msg (lStr: string);
+begin
+{$IFDEF GUI}
+        Showmessage(lStr);
+{$ELSE}
+        writeln(lStr)
+{$ENDIF}
+end;
+
+function GetStr(lPrompt: string): string;
+{$IFDEF GUI}
+var
+   lOK: boolean;
+begin
+    lOK := InputQuery(lPrompt, lPrompt, result);
+    if not lOK then
+       result := '';
+end;
+{$ELSE}
+var
+   lS: string;
+begin
+      writeln ( lPrompt);
+      readln(lS);
+      result := lS;
+end;
+{$ENDIF}
+
+function GetFloat(lStr: string; lMin,lDefault,lMax: single): single;
+{$IFDEF GUI}
+var
+   s: string;
+begin
+  s := floattostr(ldefault);
+  InputQuery('Integer required',lStr,s);
+  try
+     	result := StrToFloat(S);
+  except
+    on Exception : EConvertError do
+      result := ldefault;
+  end;
+  if result < lmin then
+  	 result := lmin;
+  if result > lmax then
+  	 result := lmax;
+end;
+{$ELSE}
+var
+   lS: string;
+   lError,lI: integer;
+begin
+      writeln ( lStr+' ['+floattostr(lMin)+'..'+floattostr(lMax)+'], default '+floattostr(lDefault));
+      readln(lS);
+      Val(lS,lI,lError);
+      if lError = 0 then
+         result  := (lI)
+      else begin
+          writeln(floattostr(lDefault));
+          result := lDefault;
+      end;
+      if result < lMin then
+         result := lMin;
+      if result > lMax then
+         result := lMax;
+end;
+{$ENDIF}
+
+function GetInt(lStr: string; lMin,lDefault,lMax: integer): integer;
+{$IFDEF GUI}
+var
+   s: string;
+begin
+  s := inttostr(ldefault);
+  InputQuery('Integer required',lStr,s);
+  try
+     	result := StrToInt(S);
+  except
+    on Exception : EConvertError do
+      result := ldefault;
+  end;
+  if result < lmin then
+  	 result := lmin;
+  if result > lmax then
+  	 result := lmax;
+end;
+{$ELSE}
+var
+   lS: string;
+   lError,lI: integer;
+begin
+      writeln ( lStr+' ['+inttostr(lMin)+'..'+inttostr(lMax)+'], default '+inttostr(lDefault));
+      readln(lS);
+      Val(lS,lI,lError);
+      if lError = 0 then
+         result  := round(lI)
+      else begin
+          writeln(inttostr(lDefault));
+          result := lDefault;
+      end;
+      if result < lMin then
+         result := lMin;
+      if result > lMax then
+         result := lMax;
+end;
+{$ENDIF}
+
+
+end.
+