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bf: recon-all bad if statement
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ahoopes committed Feb 5, 2021
1 parent 98c5104 commit 290fa49
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions scripts/recon-all
Original file line number Diff line number Diff line change
Expand Up @@ -3951,11 +3951,11 @@ if($DoWhiteSurfs && ! $DoConf2Hires) then
$fs_time $cmd |& tee -a $LF
if($status) goto error_exit;
echo $cmd > $touchdir/$hemi.white.touch
if(-e $repos) then
if(-e "$repos") then
# Use json point set to reposition surface. This is a little bit of a hack
# in that the placement above is rerun even if it is not needed in order
# in that the placement above is rerun even if it is not needed in order
# to run the repositioning. This is not done for preaparc because this
# is only fine tuning
# is only fine tuning
set cmd = (mris_reposition_surface -s $white -v $bfs -p $repos -o $white)
set xopts = `fsr-getxopts ReposWhiteSurf $XOptsFile $GlobXOptsFile`;
set cmd = ($cmd $xopts)
Expand Down Expand Up @@ -4013,8 +4013,8 @@ if($DoPialSurfs && ! $DoConf2Hires) then
if($status) goto error_exit;
echo $cmd > $touchdir/$hemi.pial.touch
if($DoT2pial == 0 && $DoFLAIRpial == 0) then
cd ../surf; ln -sf $hemi.pial.T1 $hemi.pial; cd ../mri
if(-e $repos) then
cd ../surf; ln -sf $hemi.pial.T1 $hemi.pial; cd ../mri
if(-e "$repos") then
# Use json point set to reposition surface. See notes above for white.
# This is run in the T2/FLAIR stage, but it will either be done here
# or it will be done there, but not both.
Expand Down Expand Up @@ -4204,8 +4204,8 @@ if(($DoT2pial || $DoFLAIRpial) && ! $DoConf2Hires) then
if($RunIt) then
$fs_time $cmd |& tee -a $LF
if($status) goto error_exit;
cd ../surf; ln -sf $hemi.pial.$MultiModal $hemi.pial; cd ../mri
if(-e $repos) then
cd ../surf; ln -sf $hemi.pial.$MultiModal $hemi.pial; cd ../mri
if(-e "$repos") then
# Use json point set to reposition surface. See notes above for white and pial.
set cmd = (mris_reposition_surface -s $pialmm -v $bfs -p $repos -o $pialmm)
set xopts = `fsr-getxopts ReposPialSurf $XOptsFile $GlobXOptsFile`;
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