% or use (l~=0).*dat if input image was not binary Spm_write_vol(V,l~=0) % save as binary image. = sort(histc(l2(:),0:num), 1, 'descend') įprintf('Selected %d clusters (out of %d) in image.\n',length(n),num) %-Extent threshold, and sort clusters according to their extent If ~num, warning('No clusters found.') end ROIf = 'newvoi.nii' % output image (filtered on cluster size) ROI = 'myvoi.nii' % input image (binary, ie a mask) The following piece of code will read a binary mask ( ROI), perform connected component labelling, filter out all clusters under a certain size in voxel (variable k) and save it as another mask ( ROIf).
How to remove clusters under a certain size in a binary mask? Edit Spm_mesh_render('CLim',H,) % set limits to įor rendering on the three orthogonal views, use: Spm_mesh_render('CLim',H) % return current limits H = getappdata(get(findobj('Tag','SPMMeshRender'),'Parent'),'handles') If you want to specify them yourself, you can use the following piece of code. How to choose the colour limits in a rendering? Editīy default, the colour limits are such that they span min/max of the rendered data. A list of all the altered paths will be displayed at runtime. A backup of the initial file can be found in. Will update the SPM.mat file to replace all occurrence of C:\mydata with D:\Experiments\data. Spm_changepath('SPM.mat','C:\mydata','D:\Experiments\data') An utility function spm_changepath is available in SPM to replace all occurrences of one string with another within a MAT-file. If you change the location of your data and/or the SPM installation, the full paths contained in batch files and SPM.mat will be broken. How to change file paths in a batch file or SPM.mat? Edit
If you want to compute the sum instead, just use expression "sum(X)". You can also choose the output filename (say mean.img) for the mean image and its directory (default is current folder).Īlternatively, you can use the spm_mean_ui function but the number of options is limited - ImCalc should be preferred. Use the ImCalc facility with expression "mean(X)" and Data Matrix option set to "yes - read images into data matrix". How to compute the mean of a set of images? Edit You can also try to automate the process using coregistration.įor earlier versions of SPM, see Repositioning MRIs. You might also want to rotate the image such that it is better aligned with MNI space: to do so, you also need to edit the entries for the rotations (in radian) along the pitch, roll and yaw axes. This will set the origin of the image (0 0 0 mm coordinates) to AC.
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