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FSL
xtract
Commits
e20653fa
Commit
e20653fa
authored
Oct 15, 2019
by
Stamatios Sotiropoulos
Browse files
Merge branch 'patch-3' into 'master'
Add option to pass probtrackx options as a text file See merge request
!5
parents
72866ce0
77aed534
Changes
1
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xtract
View file @
e20653fa
...
...
@@ -8,9 +8,6 @@
# Protocols created by Rogier Mars et al.
#Location of CUDA binaries and libraries
#LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/cuda-7.5/lib
#export LD_LIBRARY_PATH
ptxbin_gpu
=
$FSLDIR
/bin/probtrackx2_gpu
# Location of xtract data
...
...
@@ -42,6 +39,7 @@ Usage:
-gpu Use GPU version
-native Run tractography in native (diffusion) space
-res <mm> Output resolution (Default=same as in protocol folders unless '-native' used)
-ptx_options <options.txt> Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10)
EOF
exit
1
...
...
@@ -81,6 +79,7 @@ out=""
str
=
""
p
=
""
std2diff
=
""
ptx_opts
=
""
stdref
=
"
$FSLDIR
/data/standard/MNI152_T1_1mm"
gpu
=
0
nat
=
0
...
...
@@ -99,6 +98,8 @@ while [ ! -z "$1" ];do
-gpu
)
gpu
=
1
;;
-native
)
nat
=
1
;;
-res
)
res
=
$2
;
shift
;;
-ptx_options
)
ptx_opts
=
`
cat
$2
`
;
shift
;;
*
)
echo
"Unknown option '
$1
'"
;
exit
1
;;
esac
shift
...
...
@@ -187,6 +188,9 @@ mkdir -p $out/tracts
opts
=
" -s
$bpx
/merged -m
$bpx
/nodif_brain_mask -V 1"
opts
=
"
$opts
--loopcheck --forcedir --opd --ompl --seedref=
$stdref
--sampvox=1 --randfib=1 "
# Add any user-defined ptx options
opts
=
"
$opts
$ptx_opts
"
if
[
"
$nat
"
-eq
0
]
;
then
opts
=
"
$opts
--xfm=
$std2diff
--invxfm=
$diff2std
"
fi
...
...
@@ -337,8 +341,6 @@ if [ "x$SGE_ROOT" != "x" ]; then # Submit all commands to run in parallel on th
fsl_sub
-q
long.q
-l
$out
/logs
-N
xtract
-t
$commands
else
fsl_sub
-q
$FSLGECUDAQ
-T
300
-l
$out
/logs
-N
xtract
$commands
#Submission call for the WashU GPU cluster
#qsub -l nodes=1:ppn=1:gpus=1:K20x,walltime=04:00:00,mem=8gb -N autoPtx_GPU -e $out/logs/GPUerrofile -o $out/logs/GPUoutfile $commands
fi
else
# If no SGE, run locally
sh
$commands
...
...
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