mt_prep_gamma_snap, @FeiLiu: a)line 149. From "calamp calamp.in $width $WORKDIR/calamp.out s 1 $maskfile" to "calamp calamp.in $width $WORKDIR/calamp.out f 1 $maskfile".This will influence the output file of selpsc.in, calamp.out @FeiLiu: b)line 230&232. From "mt_extract_cands 1 1 1 1 s 1 $maskfile" to "mt_extract_cands 1 1 1 1 f 1 $maskfile". This will influence the output file of pscands.1.ij, pscands.1.ij0, pscands.1.ij.int, pscands.1.da, mean_amp.flt @alvegavaleri c)lines 253-255. Add “grep -rl '/cygdrive/c' *.txt | xargs sed -i 's+/cygdrive/c+C:+g' grep -rl '/cygdrive/c' *.out | xargs sed -i 's+/cygdrive/c+C:+g' grep -rl '/cygdrive/c' *.in | xargs sed -i 's+/cygdrive/c+C:+g’” to change from the absolute path using by cygwin to the absolute path used by windows (matlab). This example works if you work in your C: drive. If you wish to use a drive with another name just modify these lines with the correct name. eg: if you work from D: drive, you have to use grep -rl '/cygdrive/d’ *.txt | xargs sed -i 's+/cygdrive/d+D:+g