Merge branch 'dev' of github.com:freesurfer/freesurfer into dev

ayendiki · Dec 19, 2020 · aef70d2 · aef70d2
2 parents c7d6508 + 334c98e
commit aef70d2
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Showing 2 changed files with 35 additions and 17 deletions.
diff --git a/scripts/groupstats b/scripts/groupstats
@@ -18,7 +18,7 @@ set aparclist = (aparc BA aparc.a2009s)
 set ASegLUT = $FREESURFER_HOME/ASegStatsLUT.txt
 set WMParcLUT = $FREESURFER_HOME/WMParcStatsLUT.txt
 set OverWrite = 0;
-set mapmeaslist = (thickness area volume curv sulc) 
+set mapmeaslist = (thickness area volume curv sulc w-g.pct) 
 set DoAparcStats = 1
 set DoAsegStats = 1
 set DoWMParcStats = 1
@@ -125,14 +125,28 @@ foreach aparc ($aparclist)
     foreach hemi ($hemilist)
       foreach meas ($mapmeaslist)
         if($meas == curv || $meas == sulc) continue # curv breaks aparcstats2table
-        set parc = $aparc
-	if($aparc == BA) set parc = BA$BAex
-        if($surf == pial) set parc = pial.$aparc; # only aparc
+        if($meas == w-g.pct && ($aparc != aparc || $surf != white)) continue 
         set outfile = $outdir/rois/$aparc.$hemi.$surf.$meas.dat
-        if(! -e $outfile || $OverWrite) then
-          set cmd = (aparcstats2table --subjects $slist --hemi $hemi \
-             -m $meas -t $outfile -p $parc)
-          echo "#C# $cmd" | tee -a $LF
+        if($meas != w-g.pct) then
+          set parc = $aparc
+          if($aparc == BA) set parc = BA$BAex
+          if($surf == pial) set parc = pial.$aparc; # only aparc
+          if(! -e $outfile || $OverWrite) then
+            set cmd = (aparcstats2table --subjects $slist --hemi $hemi \
+               -m $meas -t $outfile -p $parc)
+            echo "#C# $cmd" | tee -a $LF
+            $cmd | tee -a $LF
+            if($status) exit 1;
+            set glmdir = $outdir/rois/glm.$aparc.$hemi.$surf.$meas
+            set cmd = (mri_glmfit --table $outfile --fsgd $fsgd --glmdir $glmdir)
+            echo "#C# $cmd"  | tee -a $LF
+            $cmd | tee -a $LF
+            if($status) exit 1;
+          endif
+        else
+          set cmd = (asegstats2table --subjects $slist -m mean -t $outfile \
+            --no-segno 0 1000 2000 --statsfile=$hemi.w-g.pct.stats)
+          echo "#C# $cmd"  | tee -a $LF
           $cmd | tee -a $LF
           if($status) exit 1;
           set glmdir = $outdir/rois/glm.$aparc.$hemi.$surf.$meas
@@ -145,7 +159,8 @@ foreach aparc ($aparclist)
     end # hemi
   end # surf
 end # aparc
-endif
+
+endif #DoAparcStats
 
 # ASEG Stats ----------------------------------------------------
 if($DoAsegStats) then
@@ -207,11 +222,13 @@ endif
 # Maps and GLM ---------------------------------------
 if($DoMaps) then
   foreach meas ($mapmeaslist)
+    set fmt = ()
+    if($meas == w-g.pct) set fmt = .mgh
     foreach hemi ($hemilist)
       # concat data ---------------------
       set outfile =  $outdir/maps/$meas.$hemi.sm00.mgh
       if(! -e $outfile || $OverWrite) then
-        set cmd = (mris_preproc --meas $meas --fsgd $fsgd --hemi $hemi --o $outfile --srcsurfreg $SrcSurfReg)
+        set cmd = (mris_preproc --meas $meas$fmt --fsgd $fsgd --hemi $hemi --o $outfile --srcsurfreg $SrcSurfReg)
         echo "#C# $cmd"  | tee -a $LF
         $cmd | tee -a $LF
         if($status) exit 1;
@@ -340,7 +357,7 @@ while( $#argv != 0 )
       breaksw
 
     case "--no-wmparcstats":
-      set DoAsegStats = 0
+      set DoWMParcStats = 0
       breaksw
 
     case "--no-stats":

diff --git a/scripts/groupstatsdiff b/scripts/groupstatsdiff
@@ -85,6 +85,7 @@ foreach aparc ($aparclist)
     foreach hemi ($hemilist)
       foreach meas ($mapmeaslist)
         if($meas == curv || $meas == sulc) continue # curv breaks aparcstats2table
+        if($meas == w-g.pct && ($aparc != aparc || $surf != white)) continue 
         set Skip = 0;
         foreach nomeas ($nomeaslist)
           if($meas == $nomeas) then
@@ -106,7 +107,7 @@ foreach aparc ($aparclist)
         echo "#C# $cmd" | tee -a $LF
         $cmd | tee -a $LF
         if($status) exit 1;
-        set glmdir = $outdir/rois/glm.diff.$parc.$hemi.$surf.$meas
+        set glmdir = $outdir/rois/glm.$parc.$hemi.$surf.$meas
         set cmd = (mri_glmfit --table $difftable --glmdir $glmdir $gcmd)
         echo "#C# $cmd"  | tee -a $LF
         $cmd | tee -a $LF
@@ -131,7 +132,7 @@ foreach hemi ($hemilist other)
     echo "#C# $cmd" | tee -a $LF
     $cmd | tee -a $LF
     if($status) exit 1;
-    set glmdir = $outdir/rois/glm.diff.$b
+    set glmdir = $outdir/rois/glm.$b
     set cmd = (mri_glmfit --table $difftable --glmdir $glmdir $gcmd)
     echo "#C# $cmd"  | tee -a $LF
     $cmd | tee -a $LF
@@ -150,7 +151,7 @@ if($DoCommon) set cmd = ($cmd --common)
 echo "#C# $cmd" | tee -a $LF
 $cmd | tee -a $LF
 if($status) exit 1;
-set glmdir = $outdir/rois/glm.diff.wmparc.vol
+set glmdir = $outdir/rois/glm.wmparc.vol
 set cmd = (mri_glmfit --table $difftable --glmdir $glmdir $gcmd)
 echo "#C# $cmd"  | tee -a $LF
 $cmd | tee -a $LF
@@ -180,7 +181,7 @@ if($DoMaps) then
         $cmd | tee -a $LF
         if($status) exit 1;
         # glm ------------------------
-        set glmdir = $outdir/maps/glm.diff.$meas.$hemi.sm$fwhmstr
+        set glmdir = $outdir/maps/glm.$meas.$hemi.sm$fwhmstr
         set cmd = (mri_glmfit --surface fsaverage $hemi --y $smdifffile --glmdir $glmdir $gcmd)
         echo "#C# $cmd"  | tee -a $LF
         $cmd | tee -a $LF
@@ -381,7 +382,7 @@ endif
 set fsgd1 = $g1dir/group.fsgd
 set fsgd2 = $g2dir/group.fsgd
 set n = `diff $fsgd1 $fsgd2 | wc -l`
-if($n != 0) then
+if(0 && $n != 0) then
   echo "ERROR: fsgd files $fsgd1 and $fsgd2 are not the same"
   exit 1; 
 endif
@@ -446,7 +447,7 @@ two analyses.
 One can then evaluate the differences with something like
 
 tksurfer fsaverage lh inflated -aparc \
-   -ov diffdir/maps/glm.diff.thickness.lh.sm10/osgm/sig.mgh \
+   -ov diffdir/maps/glm.thickness.lh.sm10/osgm/sig.mgh \
    -t diffdir/maps/diff.thickness.lh.sm10.mgh
 
 The map will indicate OSGM differences and the "time" course will show