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Amy Howard
Cudimot-models
Commits
e6f754f0
Commit
e6f754f0
authored
Jul 27, 2021
by
Amy Howard
Browse files
Delete run_NODDI.sh
parent
a99c886c
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NODDI_Watson_diff/development/run_NODDI.sh
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a99c886c
#!/bin/sh
# Wrapper function to run NODDI
# AH Apr 2020
Usage
()
{
echo
""
echo
"Usage: run_NODDI.sh <subject_directory> [options]"
echo
""
echo
"expects to find data and nodif_brain_mask in subject directory"
echo
""
echo
"<options>:"
echo
"-m (model = invivo/exvivo)"
echo
"--dax (axial diffusivity) "
echo
"-Q (name of the GPU(s) queue, default cuda.q (defined in environment variable: FSLGECUDAQ)"
echo
"-NJOBS (number of jobs to queue, the data is divided in NJOBS parts, usefull for a GPU cluster, default 4)"
echo
"--runMCMC (if you want to run MCMC)"
echo
"-b (burnin period, default 5000)"
echo
"-j (number of jumps, default 1250)"
echo
"-s (sample every, default 25)"
echo
"--BIC_AIC (calculate BIC & AIC)"
echo
""
exit
1
}
[
"
$1
"
=
""
]
&&
Usage
modelname
=
NODDI_Watson
step1
=
GridSeach
step2
=
FitFractions
export
LD_LIBRARY_PATH
=
${
LD_LIBRARY_PATH
}
:
${
FSLDIR
}
/lib
subjdir
=
`
make_absolute
$1
`
subjdir
=
`
echo
$subjdir
|
sed
's/\/$/$/g'
`
echo
"---------------------------------------------------------------------------------"
echo
"------------------------------------ CUDIMOT ------------------------------------"
echo
"----------------------------- MODEL:
$modelname
-----------------------------"
echo
"---------------------------------------------------------------------------------"
echo
subjectdir is
$subjdir
start
=
`
date
+%s
`
#parse option arguments
njobs
=
4
burnin
=
1000
njumps
=
1250
sampleevery
=
25
other
=
""
queue
=
""
lastStepModelOpts
=
""
shift
while
[
!
-z
"
$1
"
]
do
case
"
$1
"
in
-Q
)
queue
=
"-q
$2
"
;
shift
;;
-NJOBS
)
njobs
=
$2
;
shift
;;
-b
)
burnin
=
$2
;
shift
;;
-j
)
njumps
=
$2
;
shift
;;
-s
)
sampleevery
=
$2
;
shift
;;
--runMCMC
)
lastStepModelOpts
=
$lastStepModelOpts
" --runMCMC"
;;
--BIC_AIC
)
lastStepModelOpts
=
$lastStepModelOpts
" --BIC_AIC"
;;
*
)
other
=
$other
" "
$1
;;
esac
shift
done
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