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Amy Howard
Cudimot-models
Commits
115346dc
Commit
115346dc
authored
Sep 09, 2021
by
Amy Howard
Browse files
Update run_NODDI.sh
parent
9d1bc3a9
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run_NODDI.sh
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115346dc
/Users/amyh/Desktop/func/run_NODDI.sh
\ No newline at end of file
#!/bin/sh
# Wrapper function to run NODDI
# Can user specify both dax and diso on either in vivo or ex vivo model
# AH Apr 2020
make_absolute
(){
dir
=
$1
;
if
[
-d
${
dir
}
]
;
then
OLDWD
=
`
pwd
`
cd
${
dir
}
dir_all
=
`
pwd
`
cd
$OLDWD
else
dir_all
=
${
dir
}
fi
echo
${
dir_all
}
}
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
"--diso (isotropic diffusivity) "
echo
"--runMCMC (if you want to run MCMC)"
echo
"--rician (if you want to run rician noise modelling during MCMC)"
echo
"--getPredictedSignal (save the predicted signal by the model at the end)"
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
subjdir
=
`
make_absolute
$1
`
module add cuda/7.5
.
/opt/fmrib/fsl/etc/fslconf/fsl.sh
export
FSLCONFDIR
=
/opt/fmrib/fsl/config
export
FSLMACHTYPE
=
linux_64-gcc4.8
export
CUDA
=
/opt/cuda-7.5
export
FSLDEVDIR
=
/home/fs0/amyh/cudimot/fsl-dev
export
CUDIMOT
=
$FSLDEVDIR
#parse option arguments
njobs
=
4
burnin
=
1000
njumps
=
1250
sampleevery
=
25
other
=
""
queue
=
""
lastStepModelOpts
=
""
model
=
invivo
mcmc
=
0
shift
while
[
!
-z
"
$1
"
]
do
case
"
$1
"
in
-m
)
model
=
$2
;
shift
;;
--dax
)
dax
=
$2
;
shift
;;
--diso
)
diso
=
$2
;
shift
;;
-b
)
burnin
=
$2
;
shift
;;
-j
)
njumps
=
$2
;
shift
;;
-s
)
sampleevery
=
$2
;
shift
;;
--runMCMC
)
mcmc
=
1
;;
--rician
)
mcmc
=
1
;
lastStepModelOpts
=
$lastStepModelOpts
" --rician"
;;
--BIC_AIC
)
lastStepModelOpts
=
$lastStepModelOpts
" --BIC_AIC"
;;
--getPredictedSignal
)
lastStepModelOpts
=
$lastStepModelOpts
" --getPredictedSignal"
;;
*
)
other
=
$other
" "
$1
;;
esac
shift
done
if
[
$mcmc
-eq
1
]
;
then
lastStepModelOpts
=
$lastStepModelOpts
" --runMCMC"
elif
[
$mcmc
-eq
0
]
;
then
echo
"Note: Rician noise modelling is not selected, though its use is recommended."
fi
if
[
-z
"
$model
"
]
;
then
echo
"Must specify model name as either 'invivo' or 'exvivo'"
exit
1
elif
[
"
$model
"
==
"invivo"
]
;
then
# Default params
if
[
-z
"
$dax
"
]
;
then
dax
=
0.0017
;
fi
if
[
-z
"
$diso
"
]
;
then
diso
=
0.003
;
fi
export
modelname
=
NODDI_Watson_diff
elif
[
"
$model
"
==
"exvivo"
]
;
then
# Default params
if
[
-z
"
$dax
"
]
;
then
dax
=
0.0006
;
fi
# No idea where these values come from
if
[
-z
"
$diso
"
]
;
then
diso
=
0.002
;
fi
export
modelname
=
NODDI_Watson_diff_exvivo
else
echo
"Must specify model name as either 'invivo' or 'exvivo'"
exit
1
fi
opts
=
"--dax
$dax
--diso
$diso
-b
$burnin
-j
$njumps
-s
$sampleevery
"
echo
Please remember to cite Hernandez-Fernandez et al. Neuroimage 1019
if
using this code.
/home/fs0/amyh/cudimot/mymodels/
$modelname
/Pipeline_
${
modelname
}
.sh
$subjdir
$opts
$lastStepModelOpts
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