diff --git a/fdtx.tcl b/fdtx.tcl
index bb7e3aa9af86172b54c0d5cea6fa33a77bb26a7b..48a6fe31ea66d3176e91ac6a3c3d13f27cb87fd1 100644
--- a/fdtx.tcl
+++ b/fdtx.tcl
@@ -733,7 +733,7 @@ proc fdt:apply { w dialog } {
 	       } 
                seedmask {
 		     if { $probtrack(bcyn) } { 
-                       fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(bedpost_dir)/nodif_brain_mask -ref $probtrack(bedpost_dir)/nodif_brain_mask -applyisoxfm 5 -out $probtrack(output)/lowresmask"
+                       fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(bedpost_dir)/nodif_brain_mask -ref $probtrack(bedpost_dir)/nodif_brain_mask -applyisoxfm $probtrack(scale) -out $probtrack(output)/lowresmask"
                        fdt_monitor_short $w "${FSLDIR}/bin/avwmaths  $probtrack(output)/lowresmask -thr 0.5 -bin  $probtrack(output)/lowresmask"
                        set flags "$flags --lrmask=$probtrack(output)/lowresmask --omatrix2" 
                    }