From 676277501f0e61405adde8854858ba27c426246b Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Wed, 11 Dec 2019 15:30:22 +0000
Subject: [PATCH] ENH: tests for multi-shell dtifit to the diffusion MRI data

Tests both kurtosis flags (also --wls with --kurt flag)
---
 diffusion_multishell/feedsInputs      | 1 +
 diffusion_multishell/feedsRun.kurt    | 9 +++++++++
 diffusion_multishell/feedsRun.kurtdir | 8 ++++++++
 3 files changed, 18 insertions(+)
 create mode 100755 diffusion_multishell/feedsInputs
 create mode 100755 diffusion_multishell/feedsRun.kurt
 create mode 100755 diffusion_multishell/feedsRun.kurtdir

diff --git a/diffusion_multishell/feedsInputs b/diffusion_multishell/feedsInputs
new file mode 100755
index 0000000..cb26881
--- /dev/null
+++ b/diffusion_multishell/feedsInputs
@@ -0,0 +1 @@
+diffusion_multishell
diff --git a/diffusion_multishell/feedsRun.kurt b/diffusion_multishell/feedsRun.kurt
new file mode 100755
index 0000000..1592f98
--- /dev/null
+++ b/diffusion_multishell/feedsRun.kurt
@@ -0,0 +1,9 @@
+#!/usr/bin/env sh
+
+# Runs dtifit with the --kurt flag on the multi-shell diffusion data
+
+outdir=$1
+datadir=$2/diffusion_multishell
+
+dtifit -k ${datadir}/data.nii.gz -b ${datadir}/bvals -r ${datadir}/bvecs -m ${datadir}/nodif_brain_mask -o ${outdir}/kurt --kurt
+dtifit -k ${datadir}/data.nii.gz -b ${datadir}/bvals -r ${datadir}/bvecs -m ${datadir}/nodif_brain_mask -o ${outdir}/kurt_wls --kurt --wls
diff --git a/diffusion_multishell/feedsRun.kurtdir b/diffusion_multishell/feedsRun.kurtdir
new file mode 100755
index 0000000..bc8653a
--- /dev/null
+++ b/diffusion_multishell/feedsRun.kurtdir
@@ -0,0 +1,8 @@
+#!/usr/bin/env sh
+
+# Runs dtifit with the --kurt flag on the multi-shell diffusion data
+
+outdir=$1
+datadir=$2/diffusion_multishell
+
+dtifit -k ${datadir}/data.nii.gz -b ${datadir}/bvals -r ${datadir}/bvecs -m ${datadir}/nodif_brain_mask -o ${outdir}/kurtdir --kurtdir
-- 
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