add atlas2nii

nii_atlas2nii.m

@@ -0,0 +1,43 @@
+function nii_atlas2nii (atlasfnm)
+%Convert NIfTI indexed atlas to series of NIfTI images, one per region
+% atlasfnm = (optional) filenames to convert, e.g. 'aal.nii.gz'
+%Examples
+% nii_atlas2nii; %use GUI
+% nii_atlas2nii('aal.nii.gz');
+
+if ~exist('atlasfnm','var') %no files specified
+ atlasfnm = spm_select(1,'^.*\.(gz|voi|img|nii)$','Select Atlas to convert');
+end;
+[niiname, isGz] = unGzSub (atlasfnm); %eg. aal.nii.gz -> aal.nii
+[p,n,~] =spm_fileparts(niiname);
+hdr = spm_vol(niiname);
+if ~spm_type(hdr.dt,'intt'), error('Atlases must have integer datatype %s\n', niiname); end;
+img = spm_read_vols(hdr);
+for i = 1 : max(img(:)) %for each region
+    imgI = img;
+    imgI(imgI ~= i) = 0; %mask images not of index value
+    imgI(imgI ~= 0) = 1; %binarize image
+    numVx = sum(imgI(:));
+    fprintf('region %d has %d voxels\n', i, numVx);
+    if numVx < 1, continue; end; %skip empty regions
+    hdr.fname = fullfile(p, [ n '_' num2str(i) '.nii']);  
+    spm_write_vol(hdr,imgI);
+end;
+if isGz %delete uncompressed image: FSL does not allow 'img.nii' and 'img.nii.gz' to exist in same folder
+    delete(niiname);
+end
+%end nii_atlas2nii()
+
+function [fnm, isGz] = unGzSub (fnm)
+isGz = false;
+[pth,nam,ext] = spm_fileparts(fnm);
+if strcmpi(ext,'.gz') %.nii.gz -> .nii
+    isGz = true;
+    fnm = char(gunzip(fnm));    
+elseif strcmpi(ext,'.voi') %.voi -> .nii
+    isGz = true;
+    onam = char(gunzip(fnm));
+    fnm = fullfile(pth, [nam '.nii']);
+    movefile(onam,fnm);
+end;  
+%end unGzSub()

nii_enat_norm.m

@@ -484,7 +484,10 @@ function coregEstTemplateSub(vols, modality)
 %matlabbatch{1}.spm.spatial.coreg.estimate.source = {'/Users/rorden/Desktop/pre/bvisiblehuman.nii,1'};
 matlabbatch{1}.spm.spatial.coreg.estimate.source = {[deblank(vols{1}),',1']};%{'/Users/rorden/Desktop/3D.nii,1'};
 if  numel(vols) > 1
-    matlabbatch{1}.spm.spatial.coreg.estimate.other = vols(2:end);% {''};
+    matlabbatch{1}.spm.spatial.coreg.estimate.other = vols(2:end);
+	if size(matlabbatch{1}.spm.spatial.coreg.estimate.other,2) > 1, %must be column
+    	matlabbatch{1}.spm.spatial.coreg.estimate.other = matlabbatch{1}.spm.spatial.coreg.estimate.other';
+	end
 else
     matlabbatch{1}.spm.spatial.coreg.estimate.other = {''};
 end

nii_reslice_target.m

@@ -1,14 +1,14 @@
 function [outhdr, outimg] = nii_reslice_target(inhdr, inimg, tarhdr, interp) 
 %Reslice input image to match dimensions of target image (either to disk or memory)
 %  inhdr: image to reslice- either filename of NIfTI header or loaded NIfTI header structure
-%  inimg: (optional) NIfTI image data (only if inhdr is a structure)
+%  inimg: (optonal) NIfTI image data (only if inhdr is a structure)
 %  tarhdr: image to match- either filename of NIfTI header or loaded NIfTI header structure
 %  interp: (optional) if 0 nearest neighbor interpolation, else trilinear interpolation (default)
 % Outputs: if not specified, resliced image saved to disk, else returns resliced header and image
 %Chris Rorden (2014) see John Ashburner and Ged Ridgway's reorient.m 
 % http://opensource.org/licenses/BSD-2-Clause
 %Examples
-%  nii_reslice_target('T1_LM1001.nii','','jhu.nii',false);
+%  nii_reslice_target('T1_LM1001.nii','','jhu.nii',0);
 % Next example shows how to use this without writing to disk
 %  inhdr = spm_vol('T1_LM1001.nii'); %load header
 %  inimg = spm_read_vols(inhdr); %load volume
@@ -38,6 +38,7 @@
 if ~exist('interp','var')
     interp = 1;%linear
 end
+if ~isnumeric(interp), interp = interp + 0; end; %change false/true to 0/1
 if ~isstruct(tarhdr)
     tarhdr = spm_vol(tarhdr); %load target header
 end

nii_zeronan.m

@@ -25,6 +25,7 @@ function nii_zeronan(fnms)
         if numNan > 0
             hdr.fname = fullfile(pth, ['z' nm ext]);  
             img(isnan(img)) = 0;%max(img(:)); % use ~isfinite instead of isnan to replace +/-inf with zero
+            %img = - img;
             spm_write_vol(hdr,img);
         end
     end