Delete NODDI_Watson_finish.sh

NODDI_Watson_diff/NODDI_Watson_finish.sh

-#!/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