Fix manedits for wm.mgz

Deep-MI · Nov 8, 2024 · 63ccb88 · 63ccb88
1 parent 4a5cac5
commit 63ccb88
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/recon_surf/recon-surf.sh b/recon_surf/recon-surf.sh
@@ -811,7 +811,7 @@ for hemi in lh rh ; do
 
   wm_file="wm.mgz"
   wm_manedit="$(add_file_suffix "$wm_file" "manedit")"
-  if [[ -e "$wm_manedit" ]] ; then wm_file="$wm_manedit" ; fi
+  if [[ -e "$mdir/$wm_manedit" ]] ; then wm_file="$wm_manedit" ; fi
 
   # In Long stream we skip topo fix
   if [ "$long" == "0" ] ; then
@@ -843,7 +843,7 @@ for hemi in lh rh ; do
 
     # for place_surfaces white.preparc we need to directly call it with special long parameter:
     # cmd="recon-all -subject $subject -hemi $hemi -white-preaparc -no-isrunning $hiresflag $fsthreads"
-    cmd="mris_place_surface --adgws-in $sdir/autodet.gw.stats.$hemi.dat --wm $mdir/wm.mgz --threads $threads --invol $mdir/brain.finalsurfs.mgz --$hemi --i $sdir/$hemi.orig --o $sdir/${hemi}.white.preaparc --white --seg $mdir/aseg.presurf.mgz --max-cbv-dist 3.5"
+    cmd="mris_place_surface --adgws-in $sdir/autodet.gw.stats.$hemi.dat --wm $mdir/$wm_file --threads $threads --invol $mdir/brain.finalsurfs.mgz --$hemi --i $sdir/$hemi.orig --o $sdir/${hemi}.white.preaparc --white --seg $mdir/aseg.presurf.mgz --max-cbv-dist 3.5"
     RunIt "$cmd" "$LF" "$CMDF"
 
   fi # long
@@ -1014,7 +1014,7 @@ for hemi in lh rh ; do
   # CREATE WHITE SURFACE:
   # 4 min compute white :
   cmd="mris_place_surface --adgws-in ../surf/autodet.gw.stats.${hemi}.dat --seg aseg.presurf.mgz \
-    --threads $threads --wm wm.mgz --invol brain.finalsurfs.mgz --$hemi --o ../surf/${hemi}.white \
+    --threads $threads --wm $wm_file --invol brain.finalsurfs.mgz --$hemi --o ../surf/${hemi}.white \
     --white --nsmooth 0 --rip-label ../label/${hemi}.cortex.label \
     --rip-bg --rip-surf ../surf/${hemi}.white.preaparc --aparc $aparc"
   if [ "$long" == "0" ] ; then # cross/regular/base
@@ -1027,7 +1027,7 @@ for hemi in lh rh ; do
   # CREAT PIAL SURFACE
   # 4 min compute pial :
   cmd="mris_place_surface --adgws-in ../surf/autodet.gw.stats.${hemi}.dat --seg aseg.presurf.mgz \
-    --threads $threads --wm wm.mgz --invol brain.finalsurfs.mgz --$hemi --o ../surf/${hemi}.pial.T1 \
+    --threads $threads --wm $wm_file --invol brain.finalsurfs.mgz --$hemi --o ../surf/${hemi}.pial.T1 \
     --pial --nsmooth 0 --rip-label ../label/${hemi}.cortex+hipamyg.label \
     --pin-medial-wall ../label/${hemi}.cortex.label --aparc $aparc \
     --repulse-surf ../surf/${hemi}.white --white-surf ../surf/${hemi}.white"