... with rendered zstat images from fsl (cf https://schluppeck.github.io/dafni/matlab_images/)
The matlab montage command can handle different colormaps, indices, etc. Check out the documentation and also have a look at the snipptes of code in montageWithRender.m, which produces acceptable results:
doc montage()| %% dealing with weird colour maps from rendered thresholded maps (FSL) | |
| % | |
| % cf: https://schluppeck.github.io/dafni/matlab_images/ | |
| % | |
| % ds 2019-04-15 | |
| % load in the file with the sepcial colormap | |
| load('renderMap.txt') | |
| % and a "merged" data set | |
| data = niftiread('rendered_thresh_zstat1.nii'); | |
| % nSamples - how many slices to put into montage | |
| nSamples = 10; | |
| theSlices = round(linspace(1,size(data,3), nSamples)); % make an integer range of slices | |
| %% now issue montage command | |
| montage(data, ... % rows <-> columns | |
| 'DisplayRange', [min(data(:)), max(data(:))], ... % make sure you display the whole range of values | |
| 'Indices', theSlices ); | |
| % and now use the funky color map for display | |
| colormap(renderMap); | |
| % now export / print(), etc as usual. |
