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Merge branch 'dev' of github.com:freesurfer/freesurfer into dev
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Douglas Greve committed Jun 16, 2021
2 parents 706f389 + 8d7c33d commit 6f98ef3
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Showing 3 changed files with 406 additions and 289 deletions.
67 changes: 36 additions & 31 deletions scripts/trac-all
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1182,39 +1182,43 @@ if ($dostats) then
set refvol = $labdir/anatorig/${segname}_mask.nii.gz
endif
set inputs = ($pathdir $refvol)
if ($xspace == mni || $xspace == rob) then
if (! $#baselist) then # Cross-sectional
set inputs = ($inputs $xfmdir/diff2$xspace.$reg.lta)
else # Longitudinal
set inputs = ($inputs $xfmdir/anatorig2$xspace.lta)
endif
else if ($xspace == cvs) then
if (! $#baselist) then # Cross-sectional
set inputs = ($inputs $xfmdir/diff2anatorig.$reg.lta)
if (-e $xfmdir/cvs/$cvswarp.m3z) then
set inputs = ($inputs $xfmdir/cvs/$cvswarp.m3z)
if (-e $pathdir/path.ref.txt) then # No need to interpolate
set inputs = ($pathdir)
else
set inputs = ($pathdir $refvol)
if ($xspace == mni || $xspace == rob) then
if (! $#baselist) then # Cross-sectional
set inputs = ($inputs $xfmdir/diff2$xspace.$reg.lta)
else # Longitudinal
set inputs = ($inputs $xfmdir/anatorig2$xspace.lta)
endif
else # Longitudinal
if (-e $xfmdir/cvs/$cvswarp.m3z) then
set inputs = ($inputs $xfmdir/cvs/$cvswarp.m3z)
else if ($xspace == cvs) then
if (! $#baselist) then # Cross-sectional
set inputs = ($inputs $xfmdir/diff2anatorig.$reg.lta)
if (-e $xfmdir/cvs/$cvswarp.m3z) then
set inputs = ($inputs $xfmdir/cvs/$cvswarp.m3z)
endif
else # Longitudinal
if (-e $xfmdir/cvs/$cvswarp.m3z) then
set inputs = ($inputs $xfmdir/cvs/$cvswarp.m3z)
endif
endif
else if ($xspace == syn) then
if (! $#baselist) then # Cross-sectional
set inputs = ($inputs $xfmdir/diff2syn.lta)
set inputs = ($inputs $xfmdir/syn_warp.m3z)
else # Longitudinal
set inputs = ($inputs $xfmdir/anatorig2syn.$reg.lta)
set inputs = ($inputs $xfmdir/syn_warp.m3z)
endif
else if ($xspace == fnt) then
if (! $#baselist) then # Cross-sectional
set inputs = ($inputs $xfmdir/diff2fsl_warp.m3z)
else # Longitudinal
set inputs = ($inputs $xfmdir/anatorig2diff.$reg.lta)
set inputs = ($inputs $xfmdir/diff2fsl_warp.m3z)
endif
endif
else if ($xspace == syn) then
if (! $#baselist) then # Cross-sectional
set inputs = ($inputs $xfmdir/diff2syn.lta)
set inputs = ($inputs $xfmdir/syn_warp.m3z)
else # Longitudinal
set inputs = ($inputs $xfmdir/anatorig2syn.$reg.lta)
set inputs = ($inputs $xfmdir/syn_warp.m3z)
endif
else if ($xspace == fnt) then
if (! $#baselist) then # Cross-sectional
set inputs = ($inputs $xfmdir/diff2fsl_warp.m3z)
else # Longitudinal
set inputs = ($inputs $xfmdir/anatorig2diff.$reg.lta)
set inputs = ($inputs $xfmdir/diff2fsl_warp.m3z)
endif
endif
Expand All @@ -1234,6 +1238,7 @@ if ($dostats) then
set cmd = ($cmd --list $statdir/$pathname.$avgmode.inputs.txt)
set cmd = ($cmd --ref $intertrg)
set cmd = ($cmd --out $statdir/$pathname.$avgmode)
if ($#inputs == 1) set cmd = ($cmd --nointerp)
set LF = $statdir/$pathname.$avgmode.log
Expand Down
130 changes: 112 additions & 18 deletions scripts/trac-paths
View file
Original file line number Diff line number Diff line change
Expand Up @@ -524,6 +524,40 @@ if (! $dolong) then
@ irep = $irep + 1
end

# Create reference paths for along-tract analysis
set refdir = `dirname $trainsubjlist[1]`/$xspace
if (-d $refdir) then
set srclist = `printf "$refdir/%s.mean.trk " $pathlist`
set trglist = `printf "$outdir/%s_$avgmode/path.ref.txt " $pathlist`

# Map mean paths from template to individual
set cmd = $trcdir/dmri_trk2trk
set cmd = ($cmd --in $srclist)
set cmd = ($cmd --inref $intertrg)
if ($xspace == mni || $xspace == rob) then
set cmd = ($cmd --reg $xfmdir/diff2$xspace.$reg.lta)
else if ($xspace == cvs) then
set cmd = ($cmd --reg $xfmdir/diff2anatorig.$reg.lta)
if ($subj != $cvstemp) then
set cmd = ($cmd --regnl $xfmdir/cvs/$cvswarp.m3z)
endif
else if ($xspace == syn) then
set cmd = ($cmd --reg $xfmdir/diff2syn.lta)
set cmd = ($cmd --regnl $xfmdir/syn_warp.m3z)
else if ($xspace == fnt) then
set cmd = ($cmd --regnl $xfmdir/diff2fsl_warp.m3z)
endif
set cmd = ($cmd --inv)
set cmd = ($cmd --smooth)
set cmd = ($cmd --outasc $trglist)
set cmd = ($cmd --outref $dwidir/dtifit_FA.nii.gz)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$fs_time $cmd |& tee -a $LF
if ($status) goto error_exit
endif
endif

foreach pathname ($pathlist)
set pathpre = ${pathname}_$avgmode

Expand All @@ -537,6 +571,9 @@ if (! $dolong) then
set cmd = ($cmd --dtbase $dwidir/dtifit)
set cmd = ($cmd --path $pname)
set cmd = ($cmd --subj $subj)
if (-e $outdir/$pathpre/path.ref.txt) then
set cmd = ($cmd --invox path.ref.txt)
endif
set cmd = ($cmd --out $outdir/$pathpre/pathstats.overall.txt)
set cmd = ($cmd --outvox $outdir/$pathpre/pathstats.byvoxel.txt)
echo $cmd |& tee -a $LF |& tee -a $CF
Expand Down Expand Up @@ -584,7 +621,7 @@ if (! $dolong) then
set cmd = ($cmd --hemi $hemi)
set cmd = ($cmd --projdist-avg $projmin $projmax $dproj)
set cmd = ($cmd --trgsubject $subj)
set cmd = ($cmd --o $outdir/$pathpre/end$pt.surf.mgz)
set cmd = ($cmd --o $outdir/$pathpre/endpt$pt.surf.mgz)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
Expand All @@ -594,9 +631,9 @@ if (! $dolong) then
set nproj = `echo "($projmax - ($projmin))/$dproj + 1" | bc -l`

set cmd = fscalc
set cmd = ($cmd $outdir/$pathpre/end$pt.surf.mgz)
set cmd = ($cmd $outdir/$pathpre/endpt$pt.surf.mgz)
set cmd = ($cmd mul $nproj)
set cmd = ($cmd --o $outdir/$pathpre/end$pt.surf.mgz)
set cmd = ($cmd --o $outdir/$pathpre/endpt$pt.surf.mgz)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
Expand All @@ -605,8 +642,8 @@ if (! $dolong) then

set cmd = mri_binarize
set cmd = ($cmd --min 1)
set cmd = ($cmd --i $outdir/$pathpre/end$pt.surf.mgz)
set cmd = ($cmd --o $outdir/$pathpre/end$pt.surf.bin.mgz)
set cmd = ($cmd --i $outdir/$pathpre/endpt$pt.surf.mgz)
set cmd = ($cmd --o $outdir/$pathpre/endpt$pt.surf.bin.mgz)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
Expand All @@ -617,9 +654,9 @@ if (! $dolong) then
if ($nvert == 0) continue

set cmd = mri_cor2label
set cmd = ($cmd --i $outdir/$pathpre/end$pt.surf.bin.mgz)
set cmd = ($cmd --i $outdir/$pathpre/endpt$pt.surf.bin.mgz)
set cmd = ($cmd --id 1)
set cmd = ($cmd --l $outdir/$pathpre/end$pt.surf.label)
set cmd = ($cmd --l $outdir/$pathpre/endpt$pt.surf.label)
set cmd = ($cmd --surf $subj $hemi white)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
Expand All @@ -628,10 +665,20 @@ if (! $dolong) then
endif

set cmd = mri_label2label
set cmd = ($cmd --srclabel $outdir/$pathpre/end$pt.surf.label)
set cmd = ($cmd --srclabel $outdir/$pathpre/endpt$pt.surf.label)
set cmd = ($cmd --s $subj --hemi $hemi --regmethod surface)
set cmd = ($cmd --dilate 5 --erode 5)
set cmd = ($cmd --trglabel $outdir/$pathpre/end$pt.surf.label)
set cmd = ($cmd --trglabel $outdir/$pathpre/endpt$pt.surf.label)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
if ($status) goto error_exit
endif

set cmd = mris_anatomical_stats
set cmd = ($cmd -l $outdir/$pathpre/endpt$pt.surf.label)
set cmd = ($cmd -f $outdir/$pathpre/endpt$pt.surf.stats)
set cmd = ($cmd $subj $hemi)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
Expand Down Expand Up @@ -932,6 +979,40 @@ else
set xfmdir_t = $dwidir_t/xfms
set outdir_t = $dtroot/$subj_t/$outdir

# Create reference paths for along-tract analysis
set refdir = `dirname $trainsubjlist[1]`/$xspace
if (-d $refdir) then
set srclist = `printf "$refdir/%s.mean.trk " $pathlist`
set trglist = `printf "$outdir_t/%s_$avgmode/path.ref.txt " $pathlist`

# Map mean paths from template to individual
set cmd = $trcdir/dmri_trk2trk
set cmd = ($cmd --in $srclist)
set cmd = ($cmd --inref $intertrg)
if ($xspace == mni || $xspace == rob) then
set cmd = ($cmd --reg $xfmdir_t/diff2$xspace.$reg.lta)
else if ($xspace == cvs) then
set cmd = ($cmd --reg $xfmdir_t/diff2anatorig.$reg.lta)
if ($subj != $cvstemp) then
set cmd = ($cmd --regnl $xfmdir_t/cvs/$cvswarp.m3z)
endif
else if ($xspace == syn) then
set cmd = ($cmd --reg $xfmdir_t/diff2syn.lta)
set cmd = ($cmd --regnl $xfmdir_t/syn_warp.m3z)
else if ($xspace == fnt) then
set cmd = ($cmd --regnl $xfmdir_t/diff2fsl_warp.m3z)
endif
set cmd = ($cmd --inv)
set cmd = ($cmd --smooth)
set cmd = ($cmd --outasc $trglist)
set cmd = ($cmd --outref $dwidir_t/dtifit_FA.nii.gz)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$fs_time $cmd |& tee -a $LF
if ($status) goto error_exit
endif
endif

foreach pathname ($pathlist)
set pathdir = $outdir_t/${pathname}_$avgmode

Expand All @@ -945,6 +1026,9 @@ else
set cmd = ($cmd --dtbase $dwidir_t/dtifit)
set cmd = ($cmd --path $pname)
set cmd = ($cmd --subj $subj_t)
if (-e $pathdir/path.ref.txt) then
set cmd = ($cmd --invox path.ref.txt)
endif
set cmd = ($cmd --out $pathdir/pathstats.overall.txt)
set cmd = ($cmd --outvox $pathdir/pathstats.byvoxel.txt)
echo $cmd |& tee -a $LF |& tee -a $CF
Expand Down Expand Up @@ -992,7 +1076,7 @@ else
set cmd = ($cmd --hemi $hemi)
set cmd = ($cmd --projdist-avg $projmin $projmax $dproj)
set cmd = ($cmd --trgsubject $subj_t)
set cmd = ($cmd --o $pathdir/end$pt.surf.mgz)
set cmd = ($cmd --o $pathdir/endpt$pt.surf.mgz)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
Expand All @@ -1002,9 +1086,9 @@ else
set nproj = `echo "($projmax - ($projmin))/$dproj + 1" | bc -l`

set cmd = fscalc
set cmd = ($cmd $pathdir/end$pt.surf.mgz)
set cmd = ($cmd $pathdir/endpt$pt.surf.mgz)
set cmd = ($cmd mul $nproj)
set cmd = ($cmd --o $pathdir/end$pt.surf.mgz)
set cmd = ($cmd --o $pathdir/endpt$pt.surf.mgz)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
Expand All @@ -1013,8 +1097,8 @@ else

set cmd = mri_binarize
set cmd = ($cmd --min 1)
set cmd = ($cmd --i $pathdir/end$pt.surf.mgz)
set cmd = ($cmd --o $pathdir/end$pt.surf.bin.mgz)
set cmd = ($cmd --i $pathdir/endpt$pt.surf.mgz)
set cmd = ($cmd --o $pathdir/endpt$pt.surf.bin.mgz)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
Expand All @@ -1025,9 +1109,9 @@ else
if ($nvert == 0) continue

set cmd = mri_cor2label
set cmd = ($cmd --i $pathdir/end$pt.surf.bin.mgz)
set cmd = ($cmd --i $pathdir/endpt$pt.surf.bin.mgz)
set cmd = ($cmd --id 1)
set cmd = ($cmd --l $pathdir/end$pt.surf.label)
set cmd = ($cmd --l $pathdir/endpt$pt.surf.label)
set cmd = ($cmd --surf $subj_t $hemi white)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
Expand All @@ -1036,10 +1120,20 @@ else
endif

set cmd = mri_label2label
set cmd = ($cmd --srclabel $pathdir/end$pt.surf.label)
set cmd = ($cmd --srclabel $pathdir/endpt$pt.surf.label)
set cmd = ($cmd --s $subj_t --hemi $hemi --regmethod surface)
set cmd = ($cmd --dilate 5 --erode 5)
set cmd = ($cmd --trglabel $pathdir/end$pt.surf.label)
set cmd = ($cmd --trglabel $pathdir/endpt$pt.surf.label)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
if ($status) goto error_exit
endif

set cmd = mris_anatomical_stats
set cmd = ($cmd -l $pathdir/endpt$pt.surf.label)
set cmd = ($cmd -f $pathdir/endpt$pt.surf.stats)
set cmd = ($cmd $subj $hemi)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
Expand Down
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