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Dev hotfix2.3.2 (#601)
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* remove zero lines in wmparc.DKTatlas.mapped.stats
* run aseg stats also for -fsaparc
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@m-reuter
m-reuter authored Oct 31, 2024
1 parent 898579e commit 770a14c
Showing 1 changed file with 53 additions and 54 deletions.
107 changes: 53 additions & 54 deletions recon_surf/recon-surf.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -1165,61 +1165,60 @@ if [ "$base" != "1" ] ; then

# ============================= FASTSURFER - STATS =========================================

if [ "$fsaparc" == "0" ] ; then
# get stats for the aseg (note these are surface fine tuned, that may be good or bad, below we also do the stats for the input aseg (plus some processing)
# cmd="recon-all -subject $subject -segstats $hiresflag $fsthreads"
if [[ "$segstats_legacy" == "true" ]] ; then
cmda=($python "$FASTSURFER_HOME/FastSurferCNN/mri_brainvol_stats.py"
--subject "$subject")
run_it "$LF" "${cmda[@]}"

cmda=($python "$FASTSURFER_HOME/FastSurferCNN/mri_segstats.py" --seed 1234
--seg "$mdir/aseg.mgz" --sum "$statsdir/aseg.stats" --pv "$mdir/norm.mgz"
"--in-intensity-name" norm "--in-intensity-units" MR --subject "$subject"
--surf-wm-vol --ctab "$FREESURFER_HOME/ASegStatsLUT.txt" --etiv
--threads "$threads")
# cmd="$python $FASTSURFER_HOME/FastSurferCNN/mri_segstats.py --seed 1234 --seg $mdir/wmparc.mgz --sum $statsdir/wmparc.stats --pv $mdir/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject $subject --surf-wm-vol --ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv"
else
# calculate brainvol stats and aseg stats with segstats.py
cmda=($python "$FASTSURFER_HOME/FastSurferCNN/segstats.py" --sid "$subject"
--segfile "$mdir/aseg.mgz" --segstatsfile "$statsdir/aseg.stats"
--pvfile "$mdir/norm.mgz" --normfile "$mdir/norm.mgz" --threads "$threads"
# --excl-ctxgmwm: exclude Left/Right WM / Cortex despite ASegStatsLUT.txt
--excludeid 0 2 3 41 42
--lut "$FREESURFER_HOME/ASegStatsLUT.txt" --empty
measures --compute "BrainSeg" "BrainSegNotVent" "VentricleChoroidVol"
"lhCortex" "rhCortex" "Cortex" "lhCerebralWhiteMatter"
"rhCerebralWhiteMatter" "CerebralWhiteMatter"
"SubCortGray" "TotalGray" "SupraTentorial"
"SupraTentorialNotVent" "Mask($mask)"
"BrainSegVol-to-eTIV" "MaskVol-to-eTIV")
if [ "$long" == "0" ] ; then
# in long we do not have orig_nofix for surface hole computation as surfaces
# are inherited from base/template
cmda+=("lhSurfaceHoles" "rhSurfaceHoles" "SurfaceHoles")
fi
cmda+=("EstimatedTotalIntraCranialVol")
run_it "$LF" "${cmda[@]}"
echo "Extract the brainvol stats section from segstats output." | tee -a "$LF"
# ... so stats/brainvol.stats also exists (but it is slightly different
# cmd="recon-all -subject $subject -segstats $hiresflag $fsthreads"
# RunIt "$cmd" "$LF"

# this call is only "required" to "compute" brainvol.stats, so --normfile/--pvfile
# are not required
cmda=($python "$FASTSURFER_HOME/FastSurferCNN/segstats.py" --sid "$subject"
--segfile "$mdir/aseg.mgz" --pvfile "$mdir/norm.mgz"
--measure_only --threads "$threads" --segstatsfile "$statsdir/brainvol.stats"
measures --file "$statsdir/aseg.stats"
--import "BrainSeg" "BrainSegNotVent" "SupraTentorial"
"SupraTentorialNotVent" "SubCortGray" "lhCortex" "rhCortex"
"Cortex" "TotalGray" "lhCerebralWhiteMatter"
"rhCerebralWhiteMatter" "CerebralWhiteMatter" "Mask"
--compute "SupraTentorialNotVentVox" "BrainSegNotVentSurf"
"VentricleChoroidVol")
# get stats for the aseg (note these are surface fine tuned, that may be good or bad, below we also do the stats for the input aseg (plus some processing)
# cmd="recon-all -subject $subject -segstats $hiresflag $fsthreads"
if [[ "$segstats_legacy" == "true" ]] ; then
cmda=($python "$FASTSURFER_HOME/FastSurferCNN/mri_brainvol_stats.py"
--subject "$subject")
run_it "$LF" "${cmda[@]}"

cmda=($python "$FASTSURFER_HOME/FastSurferCNN/mri_segstats.py" --seed 1234
--seg "$mdir/aseg.mgz" --sum "$statsdir/aseg.stats" --pv "$mdir/norm.mgz"
"--in-intensity-name" norm "--in-intensity-units" MR --subject "$subject"
--surf-wm-vol --ctab "$FREESURFER_HOME/ASegStatsLUT.txt" --etiv
--threads "$threads")
# cmd="$python $FASTSURFER_HOME/FastSurferCNN/mri_segstats.py --seed 1234 --seg $mdir/wmparc.mgz --sum $statsdir/wmparc.stats --pv $mdir/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject $subject --surf-wm-vol --ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv"
else
# calculate brainvol stats and aseg stats with segstats.py
cmda=($python "$FASTSURFER_HOME/FastSurferCNN/segstats.py" --sid "$subject"
--segfile "$mdir/aseg.mgz" --segstatsfile "$statsdir/aseg.stats"
--pvfile "$mdir/norm.mgz" --normfile "$mdir/norm.mgz" --threads "$threads"
# --excl-ctxgmwm: exclude Left/Right WM / Cortex despite ASegStatsLUT.txt
--excludeid 0 2 3 41 42
--lut "$FREESURFER_HOME/ASegStatsLUT.txt" --empty
measures --compute "BrainSeg" "BrainSegNotVent" "VentricleChoroidVol"
"lhCortex" "rhCortex" "Cortex" "lhCerebralWhiteMatter"
"rhCerebralWhiteMatter" "CerebralWhiteMatter"
"SubCortGray" "TotalGray" "SupraTentorial"
"SupraTentorialNotVent" "Mask($mask)"
"BrainSegVol-to-eTIV" "MaskVol-to-eTIV")
if [ "$long" == "0" ] ; then
# in long we do not have orig_nofix for surface hole computation as surfaces
# are inherited from base/template
cmda+=("lhSurfaceHoles" "rhSurfaceHoles" "SurfaceHoles")
fi
cmda+=("EstimatedTotalIntraCranialVol")
run_it "$LF" "${cmda[@]}"

echo "Extract the brainvol stats section from segstats output." | tee -a "$LF"
# ... so stats/brainvol.stats also exists (but it is slightly different
# cmd="recon-all -subject $subject -segstats $hiresflag $fsthreads"
# RunIt "$cmd" "$LF"
# this call is only "required" to "compute" brainvol.stats, so --normfile/--pvfile
# are not required
cmda=($python "$FASTSURFER_HOME/FastSurferCNN/segstats.py" --sid "$subject"
--segfile "$mdir/aseg.mgz" --pvfile "$mdir/norm.mgz"
--measure_only --threads "$threads" --segstatsfile "$statsdir/brainvol.stats"
measures --file "$statsdir/aseg.stats"
--import "BrainSeg" "BrainSegNotVent" "SupraTentorial"
"SupraTentorialNotVent" "SubCortGray" "lhCortex" "rhCortex"
"Cortex" "TotalGray" "lhCerebralWhiteMatter"
"rhCerebralWhiteMatter" "CerebralWhiteMatter" "Mask"
--compute "SupraTentorialNotVentVox" "BrainSegNotVentSurf"
"VentricleChoroidVol")
fi
run_it "$LF" "${cmda[@]}"


# ============================= MAPPED-WMPARC =========================================
{
Expand Down Expand Up @@ -1255,7 +1254,7 @@ if [ "$base" != "1" ] ; then
cmd="mri_surf2volseg --o $mdir/wmparc.DKTatlas.mapped.mgz --label-wm --i $mdir/aparc.DKTatlas+aseg.mapped.mgz --threads $threads --lh-annot $ldir/lh.aparc.DKTatlas.mapped.annot 3000 --lh-cortex-mask $ldir/lh.cortex.label --lh-white $sdir/lh.white --lh-pial $sdir/lh.pial --rh-annot $ldir/rh.aparc.DKTatlas.mapped.annot 4000 --rh-cortex-mask $ldir/rh.cortex.label --rh-white $sdir/rh.white --rh-pial $sdir/rh.pial"
RunIt "$cmd" "$LF"

# takes a few mins
# stats of the wmparc DKTatlas mapped
#cmd="mri_segstats --seed 1234 --seg $mdir/wmparc.DKTatlas.mapped.mgz --sum $mdir/../stats/wmparc.DKTatlas.mapped.stats --pv $mdir/norm.mgz --excludeid 0 --brainmask $mdir/brainmask.mgz --in $mdir/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject $subject --surf-wm-vol --ctab $FREESURFER_HOME/WMParcStatsLUT.txt"
if [[ "$segstats_legacy" == "true" ]] ; then
cmda=($python "$FASTSURFER_HOME/FastSurferCNN/mri_segstats.py"
Expand All @@ -1271,7 +1270,7 @@ if [ "$base" != "1" ] ; then
--sid "$subject" --sd "$SUBJECTS_DIR" --pvfile "$mdir/norm.mgz"
--segfile "$mdir/wmparc.DKTatlas.mapped.mgz" --normfile "$mdir/norm.mgz"
--lut "$FREESURFER_HOME/WMParcStatsLUT.txt" --threads "$threads"
--segstatsfile "$statsdir/wmparc.DKTatlas.mapped.stats" --empty
--segstatsfile "$statsdir/wmparc.DKTatlas.mapped.stats"
--volume_precision 1
measures --file "$statsdir/brainvol.stats" --import "Mask"
"VentricleChoroidVol" "rhCerebralWhiteMatter" "lhCerebralWhiteMatter"
Expand Down

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