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Amy Howard
Cudimot-models
Commits
112fb579
Commit
112fb579
authored
Jul 27, 2021
by
Amy Howard
Browse files
Delete NODDI_Watson_finish.sh
parent
8bc93897
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NODDI_Watson_diff/NODDI_Watson_finish.sh
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8bc93897
#!/bin/sh
#
# Moises Hernandez-Fernandez - FMRIB Image Analysis Group
#
# Copyright (C) 2004 University of Oxford
#
# SHCOPYRIGHT
Usage
()
{
echo
""
echo
"Usage: NODDI_Watson_finish <subject_directory>"
echo
""
echo
"expects to find all the estimatedParameters in subject directory"
echo
""
exit
1
}
[
"
$1
"
=
""
]
&&
Usage
directory
=
$1
cd
${
directory
}
mv
$directory
/Param_0_samples.nii.gz
$directory
/fiso_samples.nii.gz
mv
$directory
/Param_1_samples.nii.gz
$directory
/fintra_samples.nii.gz
mv
$directory
/Param_2_samples.nii.gz
$directory
/kappa_samples.nii.gz
# Change range???
mv
$directory
/Param_3_samples.nii.gz
$directory
/th_samples.nii.gz
mv
$directory
/Param_4_samples.nii.gz
$directory
/ph_samples.nii.gz
Two_div_pi
=
0.636619772367581
$FSLDIR
/bin/fslmaths
$directory
/fiso_samples.nii.gz
-Tmean
$directory
/mean_fiso
$FSLDIR
/bin/fslmaths
$directory
/fintra_samples.nii.gz
-Tmean
$directory
/mean_fintra
$FSLDIR
/bin/fslmaths
$directory
/kappa_samples.nii.gz
-Tmean
$directory
/mean_kappa
$FSLDIR
/bin/make_dyadic_vectors
$directory
/th_samples
$directory
/ph_samples
$directory
/nodif_brain_mask.nii.gz dyads1
${
FSLDIR
}
/bin/fslmaths
$directory
/mean_kappa
-recip
-atan
-mul
$Two_div_pi
$directory
/OD
# For postmortem model have a 5th parameter (non-attenuating dot compartment)
if
[
-f
$directory
/Param_5_samples.nii.gz
]
;
then
mv
$directory
/Param_5_samples.nii.gz
$directory
/irFrac_samples.nii.gz
$FSLDIR
/bin/fslmaths
$directory
/irFrac_samples.nii.gz
-Tmean
$directory
/mean_irFrac.nii.gz
fi
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