Commit 478762f9 authored by Amy Howard's avatar Amy Howard
Browse files


parent 87cb2e67
# Moises Hernandez-Fernandez - FMRIB Image Analysis Group
# Copyright (C) 2004 University of Oxford
Usage() {
echo ""
echo "Usage: NODDI_Watson_exvivo_finish <subject_directory>"
echo ""
echo "expects to find all the estimatedParameters and nodif_brain_mask in subject directory"
echo ""
exit 1
[ "$1" = "" ] && Usage
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
mv $directory/Param_3_samples.nii.gz $directory/th_samples.nii.gz
mv $directory/Param_4_samples.nii.gz $directory/ph_samples.nii.gz
mv $directory/Param_5_samples.nii.gz $directory/irFrac_samples.nii.gz
$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/irFrac_samples.nii.gz -Tmean $directory/mean_irFrac
$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
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