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FSL
xtract
Commits
93778863
Commit
93778863
authored
Jul 03, 2019
by
Saad Jbabdi
Browse files
fixed a small bug in parsing
parent
f802968e
Changes
1
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xtract
View file @
93778863
...
@@ -13,7 +13,10 @@
...
@@ -13,7 +13,10 @@
#export LD_LIBRARY_PATH
#export LD_LIBRARY_PATH
ptxbin_gpu
=
$FSLDIR
/bin/probtrackx2_gpu
ptxbin_gpu
=
$FSLDIR
/bin/probtrackx2_gpu
# Location of xtract data
datadir
=
$FSLDIR
/etc/xtract_data
# tmp dir for testing
datadir
=
/vols/Scratch/saad/xtract_data
Usage
()
{
Usage
()
{
cat
<<
EOF
cat
<<
EOF
...
@@ -68,7 +71,7 @@ while [ ! -z "$1" ];do
...
@@ -68,7 +71,7 @@ while [ ! -z "$1" ];do
-out
)
out
=
$2
;
shift
;;
-out
)
out
=
$2
;
shift
;;
-str
)
str
=
$2
;
shift
;;
-str
)
str
=
$2
;
shift
;;
-p
)
p
=
$2
;
shift
;;
-p
)
p
=
$2
;
shift
;;
-species
)
spec
=
{
$2
^^
}
;
shift
;;
# converts to uppercase
-species
)
spec
=
$2
;
shift
;;
# converts to uppercase
-stdwarp
)
std2diff
=
$2
;
diff2std
=
$3
;
shift
;
shift
;;
-stdwarp
)
std2diff
=
$2
;
diff2std
=
$3
;
shift
;
shift
;;
-gpu
)
gpu
=
1
;;
-gpu
)
gpu
=
1
;;
-native
)
nat
=
1
;;
-native
)
nat
=
1
;;
...
@@ -91,6 +94,7 @@ if [ "$std2diff" == "" ];then
...
@@ -91,6 +94,7 @@ if [ "$std2diff" == "" ];then
fi
fi
fi
fi
echo
SPECIES
$spec
# GPU stuff
# GPU stuff
...
@@ -116,7 +120,7 @@ if [ "$out" == "" ];then
...
@@ -116,7 +120,7 @@ if [ "$out" == "" ];then
errflag
=
1
errflag
=
1
fi
fi
if
[
"
$
x
spec
"
==
""
]
;
then
if
[
"
$spec
"
==
""
]
;
then
if
[
"
$str
"
==
""
]
;
then
if
[
"
$str
"
==
""
]
;
then
echo
"Must set compulsory argument '-str'"
echo
"Must set compulsory argument '-str'"
errflag
=
1
errflag
=
1
...
@@ -133,11 +137,11 @@ if [ "$xspec" == "" ];then
...
@@ -133,11 +137,11 @@ if [ "$xspec" == "" ];then
fi
fi
else
else
if
[
"
$spec
"
==
"HUMAN"
]
;
then
if
[
"
$spec
"
==
"HUMAN"
]
;
then
p
=
$
FSLDIR
/etc/fsl_autoPtx/protocols
/Human
p
=
$
datadir
/Human
str
=
$
FSLDIR
/etc/fsl_autoPtx/protocols
/structList
str
=
$
p
/struct
ure
List
elif
[
"
$spec
"
==
"MACAQUE"
]
;
then
elif
[
"
$spec
"
==
"MACAQUE"
]
;
then
p
=
$
FSLDIR
/etc/fsl_autoPtx/protocols
/Macaque
p
=
$
datadir
/Macaque
str
=
$
FSLDIR
/etc/fsl_autoPtx/protocols
/structList
str
=
$
p
/struct
ure
List
else
else
echo
"Species must be one of HUMAN or MACAQUE"
echo
"Species must be one of HUMAN or MACAQUE"
errflag
=
1
errflag
=
1
...
...
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