From 13b43e10807993a0f4c17a6ff2fb2dceca82e74d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <paulmc@fmrib.ox.ac.uk>
Date: Wed, 15 Sep 2021 09:12:28 +0100
Subject: [PATCH]  TEST: Add FSL-course-based tests for siena/sienax

---
 fsl_course/segmentation/siena/.gitkeep        |  0
 fsl_course/segmentation/siena/feedsInputs     |  1 +
 fsl_course/segmentation/siena/feedsRun.siena  | 10 ++++++++++
 fsl_course/segmentation/siena/feedsRun.sienax |  9 +++++++++
 4 files changed, 20 insertions(+)
 delete mode 100644 fsl_course/segmentation/siena/.gitkeep
 create mode 100644 fsl_course/segmentation/siena/feedsInputs
 create mode 100644 fsl_course/segmentation/siena/feedsRun.siena
 create mode 100644 fsl_course/segmentation/siena/feedsRun.sienax

diff --git a/fsl_course/segmentation/siena/.gitkeep b/fsl_course/segmentation/siena/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/fsl_course/segmentation/siena/feedsInputs b/fsl_course/segmentation/siena/feedsInputs
new file mode 100644
index 0000000..a26fa4e
--- /dev/null
+++ b/fsl_course/segmentation/siena/feedsInputs
@@ -0,0 +1 @@
+fsl_course_data/seg_struc/siena
diff --git a/fsl_course/segmentation/siena/feedsRun.siena b/fsl_course/segmentation/siena/feedsRun.siena
new file mode 100644
index 0000000..2f9c47b
--- /dev/null
+++ b/fsl_course/segmentation/siena/feedsRun.siena
@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+outdir=$1
+datadir=$2
+
+cd $outdir
+cp $datadir/sub3m0.nii.gz  .
+cp $datadir/sub3m24.nii.gz .
+
+siena sub3m0 sub3m24 -d -m -b -30 
diff --git a/fsl_course/segmentation/siena/feedsRun.sienax b/fsl_course/segmentation/siena/feedsRun.sienax
new file mode 100644
index 0000000..529ac39
--- /dev/null
+++ b/fsl_course/segmentation/siena/feedsRun.sienax
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+outdir=$1
+datadir=$2
+
+cd $outdir
+cp $datadir/sub3m0.nii.gz .
+
+sienax sub3m0 -d -b -30 -r
-- 
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