Small changes

README.md

@@ -0,0 +1,115 @@
+##### About
+
+dcm2nii is a designed to convert neuroimaging data from the NIfTI format to the DICOM format. For details and compiled versions visit the [NITRC wiki](http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage)
+
+##### Versions
+
+2-Feb-2015
+ - Support for Visual Studio
+ - Remove dependency on zlib (now uses miniz)
+
+1-Jan-2015
+ - Images separated based on TE (fieldmaps)
+ - Support for JPEG2000 using OpenJPEG or Jasper libraries
+ - Support for JPEG using NanoJPEG library
+ - Support for lossless JPEG using custom library
+
+24-Nov-2014
+ - Support for CT scans with gantry tilt and varying distance between slices
+
+11-Oct-2014
+ - Initial public release
+
+Building command line version:
+
+ This requires a C compiler. With a terminal, change directory to the 'conosle' folder and run the following: 
+
+##### DEFAULT BUILD
+
+- g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix
+
+##### ZLIB BUILD
+ If we have zlib, we can use it (-lz) and disable [miniz](https://code.google.com/p/miniz/) (-myDisableMiniZ)
+
+ - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix -lz -DmyDisableMiniZ
+
+##### MINGW BUILD
+
+If you use the (osbsolete) compiler MinGW on Windows you will want to include the rare libgcc libraries with your executable so others can use it. Here I also demonstrate the optional "-DmyDisableZLib" to remove zip support.
+
+ - g++ -O3 -s -DmyDisableOpenJPEG -DmyDisableZLib -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix  -static-libgcc
+
+
+##### JPEG2000 BUILD
+
+ If you want to build this with JPEG2000 decompression support using OpenJPEG. You will need to have the OpenJPEG 2.1 libraries installed (https://code.google.com/p/openjpeg/wiki/Installation). I suggest building static libraries...
+ svn checkout http://openjpeg.googlecode.com/svn/trunk/ openjpeg-read-only
+ cmake -DBUILD_SHARED_LIBS:bool=off .
+ make
+ sudo make install
+You should then be able to run then run:
+
+ - g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp  jpg_0XC3.cpp ujpeg.cpp -o dcm2niix -lopenjp2 
+
+But in my experience this works best if you explicitly tell the software how to find the libraries, so your compile will probably look like one of these two options:    
+
+ - g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix  -I/usr/local/include /usr/local/lib/libopenjp2.a
+
+ - g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix  -I/usr/local/lib /usr/local/lib/libopenjp2.a
+
+ If you want to build this with JPEG2000 decompression support using Jasper: You will need to have the Jasper (http://www.ece.uvic.ca/~frodo/jasper/) and libjpeg (http://www.ijg.org) libraries installed which for Linux users may be as easy as running 'sudo apt-get install libjasper-dev' (otherwise, see http://www.ece.uvic.ca/~frodo/jasper/#doc). You can then run:
+
+ - g++ -O3 -DmyDisableOpenJPEG -DmyEnableJasper -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp  -s -o dcm2niix -ljasper -ljpeg
+
+##### VISUAL STUDIO BUILD
+
+You should be able to click on the Visual Studio icons to open and build this code. Here are links for for building with [Windows XP support](http://blogs.msdn.com/b/vcblog/archive/2012/10/08/windows-xp-targeting-with-c-in-visual-studio-2012.aspx) and [64-bit support](https://msdn.microsoft.com/en-us/library/9yb4317s.aspx).
+
+##### OSX BUILD WITH BOTH 32 AND 64-BIT SUPPORT
+
+Building command line version universal binary from OSX 64 bit system:
+ This requires a C compiler. With a terminal, change directory to the 'conosle' folder and run the following: 
+
+ - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -arch i386 -o dcm2niix32
+
+ - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix64
+
+ - lipo -create dcm2niix32 dcm2niix64 -o dcm2niix
+
+ To validate that the resulting executable supports both architectures type
+
+ - file ./dcm2niix
+
+##### OSX GRAPHICAL INTERFACE BUILD
+
+Building OSX graphical user interface using XCode:
+ Copy contents of "console" folder to /xcode/dcm2/core
+ Open and compile "dcm2.xcodeproj" with XCode 4.6 or later
+
+##### THE QT AND wxWIDGETS GUIs ARE NOT YET SUPPORT - FOLLOWING LINES FOR FUTURE VERSIONS
+
+Building QT graphical user interface:
+  Open "dcm2.pro" with QTCreator. This should work on OSX and Linux. On Windows the printf information is not redirected to the user interface 
+  If compile gives you grief look at the .pro file which has notes for different operating systems.
+
+Building using wxWidgets
+wxWdigets makefiles are pretty complex and specific for your operating system. For simplicity, we will build the "clipboard" example that comes with wxwidgets and then substitute our own code. The process goes something like this.
+ a.) Install wxwdigets
+ b.) successfully "make" the samples/clipboard program
+ c.) DELETE console/makefile. WE DO NOT WANT TO OVERWRITE the WX MAKEFILE 
+ d.) with the exception of "makefile", copy the contents of console to /samples/clipboard
+ e.) overwrite the original /samples/clipboard.cpp with the dcm2niix file of the same name
+ f.) Older XCodes have problems with .cpp files, whereas wxWidgets's makefiles do not compile with "-x cpp". So the core files are called '.c' but we will rename them to .cpp for wxWidgets:
+ rename 's/\.c$/\.cpp/' *
+ g.) edit the /samples/clipboard makefile: Add "nii_dicom.o nifti1_io_core.o nii_ortho.o nii_dicom_batch.o \" to CLIPBOARD_OBJECTS:
+CLIPBOARD_OBJECTS =  \
+	nii_dicom.o nifti1_io_core.o nii_ortho.o nii_dicom_batch.o \
+	$(__clipboard___win32rc) \
+	$(__clipboard_os2_lib_res) \
+	clipboard_clipboard.o
+ h.) edit the /samples/clipboard makefile: With wxWidgets we will capture std::cout comments, not printf, so we need to add "-DDmyUseCOut" to CXXFLAGS:
+CXXFLAGS = -DmyUseCOut -DWX_PRECOMP ....
+ i.) For a full refresh
+rm clipboard
+rm *.o
+make

nii_batch12.m

@@ -17,27 +17,43 @@ function nii_batch12 (p)
 %Examples 
 
 resliceMM = 3; %resolution for reslicing data
-[fmriname, t1name, TRsec, slice_order, phase, magn, prefix] = validatePreprocSub(p);
-%0.) set origin
-%setOriginSub(strvcat(t1name, fmriname, phase, magn), 1);  %#ok<REMFF1> align images to MNI space
-%1.) motion correct, used fieldmap if specifiedclass
-[meanname, prefix] = mocoFMSub(prefix, fmriname, phase, magn);
-%2.) brain extact mean (for better coregistration)
-meanname = betSub(meanname); %brain extract mean image for better coreg
-%3.) slice-time correction
-prefix = slicetimeSub(prefix, fmriname, TRsec, slice_order); %slice-time correct
-%4.) estimate normalization, coregister and reslice fMRI
-prefix = normNewSegSub(t1name, meanname, prefix, fmriname, resliceMM);
-%5.) blur data
-prefix = smoothSub(8, prefix, fmriname); %smooth images
-%-- get rid of images we don't need
-deleteImagesSub(prefix, fmriname); %delete intermediate images
+[fmriname, t1name, TRsec, slice_order, phase, magn] = validatePreprocSub(p);
+prefix = CheckExistingPreprocess(fmriname);
+if isempty(prefix) %preprocessing not yet run 
+    %0.) set origin
+    %setOriginSub(strvcat(t1name, fmriname, phase, magn), 1);  %#ok<REMFF1> align images to MNI space
+    %1.) motion correct, used fieldmap if specifiedclass
+    [meanname, prefix] = mocoFMSub(prefix, fmriname, phase, magn);
+    %2.) brain extact mean (for better coregistration)
+    meanname = betSub(meanname); %brain extract mean image for better coreg
+    %3.) slice-time correction
+    prefix = slicetimeSub(prefix, fmriname, TRsec, slice_order); %slice-time correct
+    %4.) estimate normalization, coregister and reslice fMRI
+    prefix = normNewSegSub(t1name, meanname, prefix, fmriname, resliceMM);
+    %5.) blur data
+    prefix = smoothSub(8, prefix, fmriname); %smooth images
+    %-- get rid of images we don't need
+    deleteImagesSub(prefix, fmriname); %delete intermediate images
 %6.) compute statistics
+end;
 if ~isfield(p,'onsets'), return; end; %only if user provides details
 stat_1st_levelSub (prefix, fmriname, TRsec, p);
 %end nii_batch()
 
 %---------- LOCAL FUNCTIONS FOLLOW
+function prefix = CheckExistingPreprocess(fmriname) %originally '', if 'swa' it means we have smoothed, warped, aligned data
+prefix = '';
+nsessions = length(fmriname(:,1));
+isSWA = true;
+isSW = true;
+for s = 1 : nsessions
+    [pth,nam,ext,~] = spm_fileparts( deblank (fmriname(s,:)));
+    if ~exist(fullfile(pth,['swa', nam, ext]),'file'), isSWA = false; end;
+    if ~exist(fullfile(pth,['sw', nam, ext]), 'file'), isSW = false; end;
+end
+if isSW, prefix = 'sw'; end;
+if isSWA, prefix = 'swa'; end;
+%end
 
 function [meanname, prefix] = mocoFMSub(prefix, fmriname, phase, magn) %motion correct with field map
 if isempty(phase) || isempty(magn)
@@ -180,8 +196,15 @@ function FieldMapSub(fmriname, phase, magnitude)
    prefix = normSub( meanname, prefix, fmriname, resliceMM);
    return;
 end
-newSegSub(t1); %normalize images
-extractSub(0.01, t1, prefixSub('c1', t1), prefixSub('c2', t1));
+[p, n] = fileparts(t1);
+matname = fullfile(p, ['e' n '_seg8.mat']);
+if exist(matname, 'file')
+    fprintf('skipping normalization, using %s\n', matname);
+    extractSub(0.01, t1, prefixSub('c1e', t1), prefixSub('c2e', t1));
+else
+    matname = newSegSub(t1); %normalize images
+    extractSub(0.01, t1, prefixSub('c1', t1), prefixSub('c2', t1));
+end
 coregEstSub(prefixSub('render', t1), meanname, prefix, fmriname); %make sure fMRI is aligned with T1
 newSegWriteSub(t1, prefixSub('render', t1), '', 0.9); %reslice anatomical with 0.9mm isotropic
 newSegWriteSub(t1, meanname, '', resliceMM);
@@ -261,9 +284,12 @@ function FieldMapSub(fmriname, phase, magnitude)
 %reslice img using pre-existing new-segmentation deformation field
 if isempty(warpname) || isempty(t1name), return; end;
 [pth,nam,ext, vol] = spm_fileparts(t1name); 
-defname = fullfile(pth,['y_' nam ext]);
+defname = fullfile(pth,['y_e' nam ext]);
 if ~exist(defname,'file')
-    error('Unable to find new-segment deformation image %s',defname);
+    defname = fullfile(pth,['y_' nam ext]);
+    if ~exist(defname,'file')
+        error('Unable to find new-segment deformation image %s',defname);
+    end
 end
 warpses = getsesvolsSubFlat(prefix, warpname);
 matlabbatch{1}.spm.spatial.normalise.write.subj.def = {defname};
@@ -275,7 +301,7 @@ function FieldMapSub(fmriname, phase, magnitude)
 prefix = ['w' prefix];
 %end newsegwritesub()
 
-function newSegSub(t1, t2)
+function matname = newSegSub(t1, t2)
 %apply new segment - return name of warping matrix
 template = fullfile(spm('Dir'),'tpm','TPM.nii');
 if ~exist(template,'file')
@@ -369,7 +395,7 @@ function coregEstSub(t1, meanfmri, prefix, fmriname)
 
 %end coregEstSub()
 
-function [fmriname, t1name, TRsec, slice_order, phase, magn, prefix] = validatePreprocSub(p)
+function [fmriname, t1name, TRsec, slice_order, phase, magn] = validatePreprocSub(p)
 %check all inputs
 if exist('spm','file')~=2; fprintf('%s requires SPM\n',which(mfilename)); return; end;
 isSPM12orNewerSub; %check recent SPM
@@ -695,13 +721,15 @@ function stat_1st_levelSub (prefix, basefmriname, kTR, s)
 statpth = fullfile(pth, statdirname);
 if exist(statpth, 'file') ~= 7; mkdir(statpth); end;
 fprintf(' SPM.mat file saved in %s\n',statdirname);
+temporalderiv = false;
+hpf = 128;
 if (min([s.duration{:}]) > 5) && (max([s.duration{:}]) < 32); 
     hpf = mean([s.duration{:}]) * 4;
-	temporalderiv = false;
 	fprintf('Block design : using %.1fs high pass filter with no temporal derivative.\n',hpf);
+elseif kTR > 5.0 
+	fprintf('Sparse design : using %.1fs high pass filter without a temporal derivative.\n',hpf);
 else
     temporalderiv = true;
-    hpf = 128;
 	fprintf('Event-related design : using %.1fs high pass filter with a temporal derivative.\n',hpf);
 end;
 % MODEL SPECIFICATION

nii_clip2bb.m

@@ -35,20 +35,23 @@ function nii_clip2bb(vols, bb, clipZ, overwrite, evenXY)
 	if (mod(i,2) == 1), mmi(1) = bb(2,1); end
 	if (mod(i-1,4) < 2), mmi(2) = bb(2,2); end;
 	if (mod(i-1,8) < 4), mmi(3) = bb(2,3); end;
-	mm(i,:) = mmi;
+	mm(i,:) = mmi; %#ok<AGROW>
 end
 hdr = spm_vol([fname,',1']); %read header of 1st volume
 v2m = hdr.mat; %voxel2mm transform
 m2v=inv(v2m); %mm2voxel transform
 for i=1:size(mm,1)
-    vox(i,1:3)=mm(i,:)*m2v(1:3,1:3)' + m2v(1:3,4)';
+    vox(i,1:3)=mm(i,:)*m2v(1:3,1:3)' + m2v(1:3,4)'; %#ok<AGROW>
 end 
 mn = floor(min(vox));
 mx = ceil(max(vox));
 if ~clipZ %do not clip in Z-dimension - preserve number of slices
    mn(3) = 1;
    mx(3) = hdr.dim(3);
 end
+
+mxD = min(hdr.dim, mx);
+mnD = max([1 1 1], mn);
 if evenXY %force even number of rows and columns
 	for i = 1: 2
 		if mod(mxD(i)-mnD(i)+1,2) && mnD(i) > 1
@@ -62,8 +65,6 @@ function nii_clip2bb(vols, bb, clipZ, overwrite, evenXY)
 			fprintf('Warning: odd number of rows/columns/slices may confuse topup: %s\n', fname);
 	end
 end %if evenXY
-mxD = min(hdr.dim, mx);
-mnD = max([1 1 1], mn);
 if (max(mnD) == 1) &&  (min(hdr.dim == mxD) == 1)
 	fprintf('%s :No need to crop image\n', mfilename);
 	return;
@@ -72,13 +73,28 @@ function nii_clip2bb(vols, bb, clipZ, overwrite, evenXY)
 vx = (mxD(1)-mnD(1)+1)*(mxD(2)-mnD(2)+1)*(mxD(3)-mnD(3)+1);
 if vx <= 1, error('image not coregistered'); end;
 pct = 100* vx/(hdr.dim(1)*hdr.dim(2)*hdr.dim(3));
-fprintf('%s cropping image from %dx%dx%d -> %dx%dx%d (%g%%)\n', mfilename, hdr.dim(1), hdr.dim(2), hdr.dim(3), mxD(1)-mnD(1)+1,mxD(2)-mnD(2)+1, mxD(3)-mnD(3)+1, pct);
+h.dim = hdr.dim;
+fprintf('%s cropping image from %dx%dx%d -> %dx%dx%d (%g%%)\n', mfilename, h.dim(1), h.dim(2), h.dim(3), mxD(1)-mnD(1)+1,mxD(2)-mnD(2)+1, mxD(3)-mnD(3)+1, pct);
+for v = 1 : numel(vols) %apply parameters from first session to others
+    [pth,nam,ext, ~] = spm_fileparts(deblank(vols{v}));
+    fname = fullfile(pth,[nam ext]); %strip volume label
+    hdr = spm_vol([fname,',1']); %read header of 1st volume
+    if (h.dim(1) ~= hdr.dim(1)) || (h.dim(2) ~= hdr.dim(2)) || (h.dim(3) ~= hdr.dim(3))
+        error('%s error: Image dimensions do not match %dx%dx%d ~= %dx%dx%d %s %s', mfilename, ...
+            h.dim(1),h.dim(2),h.dim(3), hdr.dim(1),hdr.dim(2),hdr.dim(3), deblank(vols{1}), deblank(vols{v}));
+
+    end
+end
 for v = 1 : numel(vols) %apply parameters from first session to others
     [pth,nam,ext, ~] = spm_fileparts(deblank(vols{v}));
     fname = fullfile(pth,[nam ext]); %strip volume label
-    hdr = spm_vol([fname]); %read header - this time 4D if specified
+    hdr = spm_vol(fname); %read header - this time 4D if specified
     img = spm_read_vols(hdr); %load image
     hdr = spm_vol([fname,',1']); %read header of 1st volume
+    if (h.dim(1) ~= hdr.dim(1)) || (h.dim(2) ~= hdr.dim(2)) || (h.dim(3) ~= hdr.dim(3))
+        error('%s error: Image dimensions do not match %s %s', mfilename, deblank(vols{1}), deblank(vols{v}));
+
+    end
     img = img(mnD(1):mxD(1), mnD(2):mxD(2), mnD(3):mxD(3), :); %clip image dimensions
     origin= mnD*v2m(1:3,1:3)' + v2m(1:3,4)';
     hdr.mat(1:3,4) = origin;

nii_mean_stdev.m

@@ -1,8 +1,9 @@
-function nii_mean_stdev (fnms, normBrightness)
+function nii_mean_stdev (fnms, normBrightness, outname)
 %Given multiple volumes, generate mean, standard deviation, SNR maps and report unusual images. Useful for quality assurance
 % fnms : filenames to average (optional)
 % normBrightness : if false (0) raw intensity is used. if true (1) image intensity
 %                  scaled so minimum is 0 and median of non-zero voxels is 1
+% outname : optional prefix appended to output image name
 %Chris Rorden, 2014
 % http://opensource.org/licenses/BSD-2-Clause
 %SNR is mean/stdev http://www.ncbi.nlm.nih.gov/pubmed/17126038
@@ -17,6 +18,9 @@ function nii_mean_stdev (fnms, normBrightness)
 if ~exist('normBrightness','var') %no files
     normBrightness = str2double(cell2mat(inputdlg('Scale image intensity to normalize brightness? (0=no,1=yes):', 'Adjust brightness', 1,{'0'})));
 end;
+if ~exist('outname', 'var')
+    outname = '';
+end
 if size(fnms,1) < 1
     return;
 elseif size(fnms,1) == 1 %4D: compute mean and stDev using inbuilt Matlab functions
@@ -28,9 +32,9 @@ function nii_mean_stdev (fnms, normBrightness)
     error('Not enough images to estimate mean and stdev');
 end
 %save statistical images (optional)
-saveImgSub(['mean_of_' num2str(n) '.nii'],hdr,meanImg);
-saveImgSub(['stdev_of_' num2str(n) '.nii'],hdr,sdImg);
-saveImgSub(['snr_of_' num2str(n) '.nii'],hdr,meanImg ./ sdImg);
+saveImgSub([outname 'mean_of_' num2str(n) '.nii'],hdr,meanImg);
+saveImgSub([outname 'stdev_of_' num2str(n) '.nii'],hdr,sdImg);
+saveImgSub([outname 'snr_of_' num2str(n) '.nii'],hdr,meanImg ./ sdImg);
 %report mean z-score for each image
 if size(fnms,1) == 1
     reportZSub4D(meanImg, sdImg, normBrightness, fnms)