Merge pull request #430 from Deep-MI/parc

Sample Parc
Deep-MI · Jan 19, 2024 · 799fb9d · 799fb9d
2 parents 360d554 + 7cfff9f
commit 799fb9d
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diff --git a/recon_surf/recon-surf.sh b/recon_surf/recon-surf.sh
@@ -726,8 +726,8 @@ else
     RunIt "$cmd" $LF $CMDF
 
     # Rewrite surface orig.nofix to fix vertex locs bug (scannerRAS instead of surfaceRAS set with mc)
-    cmd="$python ${binpath}rewrite_mc_surface.py --input $outmesh --output $outmesh --filename_pretess $mdir/filled-pretess$hemivalue.mgz"
-    RunIt "$cmd" $LF $CMDF
+    #cmd="$python ${binpath}rewrite_mc_surface.py --input $outmesh --output $outmesh --filename_pretess $mdir/filled-pretess$hemivalue.mgz"
+    #RunIt "$cmd" $LF $CMDF
 
     # Check if the surfaceRAS was correctly set and exit otherwise (sanity check in case nibabel changes their default header behaviour)
     cmd="mris_info $outmesh | tr -s ' ' | grep -q 'vertex locs : surfaceRAS'"
@@ -818,13 +818,13 @@ echo "echo \" \"" |& tee -a $CMDF
     # this is dangerous, as some cortices could be < 0.6 mm, but then there is no volume label probably anyway.
     # Also note that currently we cannot mask non-cortex regions here, should be done in mris_anatomical stats later
     # the smoothing helps
-    cmd="mris_sample_parc -ct $FREESURFER_HOME/average/colortable_desikan_killiany.txt -file ${binpath}$hemi.DKTatlaslookup.txt -projmm 0.6 -f 5  -surf white.preaparc $subject $hemi aparc.DKTatlas+aseg.orig.mgz aparc.DKTatlas.mapped.prefix.annot"
-    RunIt "$cmd" $LF $CMDF
-
-    cmd="$python ${binpath}smooth_aparc.py --insurf $sdir/$hemi.white.preaparc --inaparc $ldir/$hemi.aparc.DKTatlas.mapped.prefix.annot --incort $ldir/$hemi.cortex.label --outaparc $ldir/$hemi.aparc.DKTatlas.mapped.annot"
+    #cmd="mris_sample_parc -ct $FREESURFER_HOME/average/colortable_desikan_killiany.txt -file ${binpath}$hemi.DKTatlaslookup.txt -projmm 0.6 -f 5  -surf white.preaparc $subject $hemi aparc.DKTatlas+aseg.orig.mgz aparc.DKTatlas.mapped.prefix.annot"
+    #RunIt "$cmd" $LF $CMDF
+    #cmd="$python ${binpath}smooth_aparc.py --insurf $sdir/$hemi.white.preaparc --inaparc $ldir/$hemi.aparc.DKTatlas.mapped.prefix.annot --incort $ldir/$hemi.cortex.label --outaparc $ldir/$hemi.aparc.DKTatlas.mapped.annot"
+    #RunIt "$cmd" $LF $CMDF
+    cmd="$python ${binpath}sample_parc.py --inseg $mdir/aparc.DKTatlas+aseg.orig.mgz --insurf $sdir/$hemi.white.preaparc --incort $ldir/$hemi.cortex.label --outaparc $ldir/$hemi.aparc.DKTatlas.mapped.annot --seglut ${binpath}$hemi.DKTatlaslookup.txt --surflut ${binpath}DKTatlaslookup.txt --projmm 0.6 --radius 2" 
     RunIt "$cmd" $LF $CMDF
 
-
 # if we segment with FS or if surface registration is requested do it here:
 if [ "$fsaparc" == "1" ] || [ "$fssurfreg" == "1" ] ; then
   echo "echo \" \"" |& tee -a $CMDF