spm_smooth

# Setup (with option to run) SPM12 smooth module using shell script 
# invoking matlab.
#
# Usage: spm_smooth otherimgfn kernel mbfn rf
#
# otherimgfn - Singular image (to be smoothed), or text filename
#              with fullpaths per row per image.
# kernel - 3d smoothing kernel. E.g. 8,8,8
# mbfn - Matlab batch output file name.
# rf - flag to run matlabbatch, 0: no, 1: yes
#
# 20220519 Created by Josh Goh.

# Assign parameters
otherimgfn=${1}
kernel=${2}
mbfn=${3}
rf=${4}

# Call matlab with input script
unset DISPLAY
matlab -nosplash > matlab.out << EOF
  settings;
  [p n e] = fileparts('${otherimgfn}');
  if strcmp(e,'.nii')
	ni = niftiinfo('${otherimgfn}');
	if length(ni.ImageSize)==4
		nvols = ni.ImageSize(4);
		for t = 1:nvols,
			temp(t).epivol = ['${otherimgfn},' num2str(t)];
		end;
		other = cellstr(strvcat(temp.epivol));
	else
		other = '${otherimgfn},1';
	end
  else
	S = textread('${otherimgfn}','%s');
	nfiles = size(S,1);
	i=1;
	for r = 1:nfiles,
		ni = niftiinfo(S{r});
		if length(ni.ImageSize)==4
			nvols = ni.ImageSize(4);
			for t = 1:nvols,
				temp(i).epivol = [deblank(S{r}) ',' num2str(t)];
				i=i+1;
			end;
		else
			temp(i).epivol = '${otherimgfn},1';
			i=i+1;
		end	
	end
	other = cellstr(strvcat(temp.epivol));
  end
  matlabbatch{1,1}.spm.spatial.smooth.data = other;
  matlabbatch{1,1}.spm.spatial.smooth.fwhm = [${kernel}];
  matlabbatch{1,1}.spm.spatial.smooth.dtype = 0;
  matlabbatch{1,1}.spm.spatial.smooth.im = 0;
  matlabbatch{1,1}.spm.spatial.smooth.prefix = 's';
  save('${mbfn}','matlabbatch');
  if ${rf},
    spm_jobman('run',matlabbatch);
  end
exit;
EOF