diff --git a/unit_tests/applyxfm4D/applyxfm4D_fail/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_fail/feedsInputs
deleted file mode 100644
index 7782318789d7b5b47150a948cb29e67c3d5a16fc..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_fail/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_fail/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_fail/feedsRun
deleted file mode 100755
index e9301f09c75e74ef4f74a70ad1b40956c1b970d8..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_fail/feedsRun
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env fslpython
-"""
-test applyxfm4D correct failure
-"""
-from subprocess import run, PIPE, CalledProcessError
-from os.path import join
-from tempfile import mkdtemp
-import os
-import sys
-
-OUTDIR = sys.argv[1]
-INDIR = sys.argv[2]
-FSLDIR = os.environ.get('FSLDIR')
-FSLBIN = join(FSLDIR, 'bin')
-# applyxfm4D fmri.nii.gz brain.nii.gz applyxfm4D_out f2b.mat -singlematrix -interp nn
-def test_applyxfm4D_fail():
- cmd = [
- join(FSLBIN, 'applyxfm4D'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
- join(OUTDIR, 'applyxfm4D_out.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_mat.mat')
- ]
- try:
- run_result = run(cmd, stdout=PIPE, check=True)
- stdout_string = run_result.stdout.decode('utf-8')
- assert False
- except CalledProcessError as e:
- print("test_applyxfm4D correctly failed. This is good!")
- assert e.returncode != 0
-
-print("running test_applyxfm4D_fail()")
-test_applyxfm4D_fail()
diff --git a/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsInputs
deleted file mode 100644
index 7782318789d7b5b47150a948cb29e67c3d5a16fc..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsRun
deleted file mode 100755
index 51fac7fb48ab8987695a9a49bd1751b99567f8d5..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsRun
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env fslpython
-"""
-test applyxfm4D matfile directory option with 4 digit numbers in filenames
-"""
-from subprocess import run, PIPE
-from os.path import join
-from tempfile import mkdtemp
-import os
-import sys
-
-OUTDIR = sys.argv[1]
-INDIR = sys.argv[2]
-FSLDIR = os.environ.get('FSLDIR')
-FSLBIN = join(FSLDIR, 'bin')
-print(INDIR)
-def test_applyxfm4D_fourdigit():
- # use trilinear interp for speed
- cmd = [
- join(FSLBIN, 'applyxfm4D'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
- join(OUTDIR, 'applyxfm4D_out.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'matfiles_four_digit'),
- '-interp',
- 'trilinear',
- '-fourdigit'
- ]
- run_result = run(cmd, stdout=PIPE, check=True)
- stdout_string = run_result.stdout.decode('utf-8')
- # check that the files were written to disk
- # the brain extracted input should exist
- assert os.path.isfile(join(OUTDIR, 'applyxfm4D_out.nii.gz')) == True
-
-test_applyxfm4D_fourdigit()
diff --git a/unit_tests/applyxfm4D/applyxfm4D_in.nii.gz b/unit_tests/applyxfm4D/applyxfm4D_in.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..0dd52e2c3d36d1cdf515050b227b3746f07a9fac
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_in.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e7b83c2989851f4c800a4fcd9f66a9cd7caa130cd760d810108b6f3a769bda26
+size 58355
diff --git a/unit_tests/applyxfm4D/applyxfm4D_mat.mat b/unit_tests/applyxfm4D/applyxfm4D_mat.mat
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_mat.mat
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/applyxfm4D_nn/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_nn/feedsInputs
deleted file mode 100644
index 7782318789d7b5b47150a948cb29e67c3d5a16fc..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_nn/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_nn/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_nn/feedsRun
deleted file mode 100755
index 20073bd4c50763b30b752c75a15aaa2bfcb255ee..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_nn/feedsRun
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env fslpython
-"""
-test applyxfm4D nn interp
-"""
-from subprocess import run, PIPE
-from os.path import join
-from tempfile import mkdtemp
-import os
-import sys
-
-OUTDIR = sys.argv[1]
-INDIR = sys.argv[2]
-FSLDIR = os.environ.get('FSLDIR')
-FSLBIN = join(FSLDIR, 'bin')
-print(INDIR)
-def test_applyxfm4D_nn():
- cmd = [
- join(FSLBIN, 'applyxfm4D'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
- join(OUTDIR, 'applyxfm4D_out.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_mat.mat'),
- '-singlematrix',
- '-interp',
- 'nn'
- ]
- run_result = run(cmd, stdout=PIPE, check=True)
- stdout_string = run_result.stdout.decode('utf-8')
- # check that the files were written to disk
- # the brain extracted input should exist
- assert os.path.isfile(join(OUTDIR, 'applyxfm4D_out.nii.gz')) == True
-
-test_applyxfm4D_nn()
diff --git a/unit_tests/applyxfm4D/applyxfm4D_ref.nii.gz b/unit_tests/applyxfm4D/applyxfm4D_ref.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..a8ffd82dba8f2da1e7949597c50418702906247f
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_ref.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2a519fe29b81f5bb1346828f95318bd3bc2eddba641c465b6ee93eb8ac878a52
+size 88593
diff --git a/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsInputs
deleted file mode 100644
index 7782318789d7b5b47150a948cb29e67c3d5a16fc..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsRun
deleted file mode 100755
index 008de98efde7b929efb7719607ae0dfc40506fde..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsRun
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env fslpython
-"""
-test applyxfm4D sinc interp
-"""
-from subprocess import run, PIPE
-from os.path import join
-from tempfile import mkdtemp
-import os
-import sys
-
-OUTDIR = sys.argv[1]
-INDIR = sys.argv[2]
-FSLDIR = os.environ.get('FSLDIR')
-FSLBIN = join(FSLDIR, 'bin')
-print(INDIR)
-def test_applyxfm4D_sinc():
- cmd = [
- join(FSLBIN, 'applyxfm4D'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
- join(OUTDIR, 'applyxfm4D_out.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_mat.mat'),
- '-singlematrix',
- '-interp',
- 'sinc'
- ]
- run_result = run(cmd, stdout=PIPE, check=True)
- stdout_string = run_result.stdout.decode('utf-8')
- # check that the files were written to disk
- # the brain extracted input should exist
- assert os.path.isfile(join(OUTDIR, 'applyxfm4D_out.nii.gz')) == True
-
-test_applyxfm4D_sinc()
diff --git a/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsInputs
deleted file mode 100644
index 7782318789d7b5b47150a948cb29e67c3d5a16fc..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsRun
deleted file mode 100755
index 76ce73949b80f3787a5c5ae7a10f39f5f6ad2058..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsRun
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env fslpython
-"""
-test applyxfm4D single matrix option
-"""
-from subprocess import run, PIPE
-from os.path import join
-from tempfile import mkdtemp
-import os
-import sys
-
-OUTDIR = sys.argv[1]
-INDIR = sys.argv[2]
-FSLDIR = os.environ.get('FSLDIR')
-FSLBIN = join(FSLDIR, 'bin')
-print(INDIR)
-def test_applyxfm4D_singlematrix():
- # use nearestneighbour interp for speed
- cmd = [
- join(FSLBIN, 'applyxfm4D'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
- join(OUTDIR, 'applyxfm4D_out.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_mat.mat'),
- '-singlematrix',
- '-interp',
- 'nn'
- ]
- run_result = run(cmd, stdout=PIPE, check=True)
- stdout_string = run_result.stdout.decode('utf-8')
- # check that the files were written to disk
- # the brain extracted input should exist
- assert os.path.isfile(join(OUTDIR, 'applyxfm4D_out.nii.gz')) == True
-
-test_applyxfm4D_singlematrix()
diff --git a/unit_tests/applyxfm4D/applyxfm4D_spline/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_spline/feedsInputs
deleted file mode 100644
index 7782318789d7b5b47150a948cb29e67c3d5a16fc..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_spline/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_spline/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_spline/feedsRun
deleted file mode 100755
index c9d20466560a1a6e664a5bb4d6225f8836725ba5..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_spline/feedsRun
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env fslpython
-"""
-test applyxfm4D spline interp
-"""
-from subprocess import run, PIPE
-from os.path import join
-from tempfile import mkdtemp
-import os
-import sys
-
-OUTDIR = sys.argv[1]
-INDIR = sys.argv[2]
-FSLDIR = os.environ.get('FSLDIR')
-FSLBIN = join(FSLDIR, 'bin')
-print(INDIR)
-def test_applyxfm4D_spline():
- cmd = [
- join(FSLBIN, 'applyxfm4D'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
- join(OUTDIR, 'applyxfm4D_out.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_mat.mat'),
- '-singlematrix',
- '-interp',
- 'spline'
- ]
- run_result = run(cmd, stdout=PIPE, check=True)
- stdout_string = run_result.stdout.decode('utf-8')
- # check that the files were written to disk
- # the brain extracted input should exist
- assert os.path.isfile(join(OUTDIR, 'applyxfm4D_out.nii.gz')) == True
-
-test_applyxfm4D_spline()
diff --git a/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsInputs
deleted file mode 100644
index 7782318789d7b5b47150a948cb29e67c3d5a16fc..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsRun
deleted file mode 100755
index 69428e8fdb0a556c3786c710e9b7288df617f8d1..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsRun
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env fslpython
-"""
-test applyxfm4D matfile directory option
-"""
-from subprocess import run, PIPE
-from os.path import join
-from tempfile import mkdtemp
-import os
-import sys
-
-OUTDIR = sys.argv[1]
-INDIR = sys.argv[2]
-FSLDIR = os.environ.get('FSLDIR')
-FSLBIN = join(FSLDIR, 'bin')
-print(INDIR)
-def test_applyxfm4D_transdir():
- # use trilinear interp for speed
- cmd = [
- join(FSLBIN, 'applyxfm4D'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
- join(OUTDIR, 'applyxfm4D_out.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'matfiles_five_digit'),
- '-interp',
- 'trilinear'
- ]
- run_result = run(cmd, stdout=PIPE, check=True)
- stdout_string = run_result.stdout.decode('utf-8')
- # check that the files were written to disk
- # the brain extracted input should exist
- assert os.path.isfile(join(OUTDIR, 'applyxfm4D_out.nii.gz')) == True
-
-test_applyxfm4D_transdir()
diff --git a/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsInputs
deleted file mode 100644
index 7782318789d7b5b47150a948cb29e67c3d5a16fc..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsRun
deleted file mode 100755
index 285e95ff6bc4004a3da4d654471a7c86a58ea0fd..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsRun
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env fslpython
-"""
-test applyxfm4D trilinear interp
-"""
-from subprocess import run, PIPE
-from os.path import join
-from tempfile import mkdtemp
-import os
-import sys
-
-OUTDIR = sys.argv[1]
-INDIR = sys.argv[2]
-FSLDIR = os.environ.get('FSLDIR')
-FSLBIN = join(FSLDIR, 'bin')
-print(INDIR)
-def test_applyxfm4D_trilinear():
- cmd = [
- join(FSLBIN, 'applyxfm4D'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
- join(OUTDIR, 'applyxfm4D_out.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_mat.mat'),
- '-singlematrix',
- '-interp',
- 'trilinear'
- ]
- run_result = run(cmd, stdout=PIPE, check=True)
- stdout_string = run_result.stdout.decode('utf-8')
- # check that the files were written to disk
- # the brain extracted input should exist
- assert os.path.isfile(join(OUTDIR, 'applyxfm4D_out.nii.gz')) == True
-
-test_applyxfm4D_trilinear()
diff --git a/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsInputs
deleted file mode 100644
index 7782318789d7b5b47150a948cb29e67c3d5a16fc..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsRun
deleted file mode 100755
index 1679e821b791be1e28eb3b995af13b2d0ccd1c9b..0000000000000000000000000000000000000000
--- a/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsRun
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env fslpython
-"""
-test applyxfm4D matfile directory option with user prefix
-"""
-from subprocess import run, PIPE
-from os.path import join
-from tempfile import mkdtemp
-import os
-import sys
-
-OUTDIR = sys.argv[1]
-INDIR = sys.argv[2]
-FSLDIR = os.environ.get('FSLDIR')
-FSLBIN = join(FSLDIR, 'bin')
-print(INDIR)
-def test_applyxfm4D_userprefix():
- # use trilinear interp for speed
- cmd = [
- join(FSLBIN, 'applyxfm4D'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
- join(OUTDIR, 'applyxfm4D_out.nii.gz'),
- join(INDIR, 'unit_tests', 'applyxfm4D', 'matfiles_user_prefix'),
- '-interp',
- 'trilinear',
- '-userprefix',
- 'myprefix_'
- ]
- run_result = run(cmd, stdout=PIPE, check=True)
- stdout_string = run_result.stdout.decode('utf-8')
- # check that the files were written to disk
- # the brain extracted input should exist
- assert os.path.isfile(join(OUTDIR, 'applyxfm4D_out.nii.gz')) == True
-
-test_applyxfm4D_userprefix()
diff --git a/unit_tests/applyxfm4D/feedsRun.fail b/unit_tests/applyxfm4D/feedsRun.fail
new file mode 100755
index 0000000000000000000000000000000000000000..b3b7ba11145510c9f69511e99a7985c0abc1cd9a
--- /dev/null
+++ b/unit_tests/applyxfm4D/feedsRun.fail
@@ -0,0 +1,21 @@
+#!/usr/bin/env fslpython
+"""
+test applyxfm4D correct failure
+"""
+import sys
+from subprocess import run, CalledProcessError
+from os.path import join
+
+OUTDIR = sys.argv[1]
+cmd = [
+ 'applyxfm4D',
+ 'applyxfm4D_in.nii.gz',
+ 'applyxfm4D_ref.nii.gz',
+ join(OUTDIR, 'applyxfm4D_out.nii.gz'),
+ 'applyxfm4D_mat.mat']
+try:
+ run(cmd, check=True)
+ assert False
+except CalledProcessError as e:
+ print("test_applyxfm4D correctly failed. This is good!")
+ assert e.returncode != 0
diff --git a/unit_tests/applyxfm4D/feedsRun.fourdigit b/unit_tests/applyxfm4D/feedsRun.fourdigit
new file mode 100755
index 0000000000000000000000000000000000000000..38aa1e3364450dc8b30bf4efb040363aa8d50cc0
--- /dev/null
+++ b/unit_tests/applyxfm4D/feedsRun.fourdigit
@@ -0,0 +1,19 @@
+#!/usr/bin/env fslpython
+"""
+test applyxfm4D matfile directory option with 4 digit numbers in filenames
+"""
+import sys
+from subprocess import run
+from os.path import join
+
+OUTDIR = sys.argv[1]
+cmd = [
+ 'applyxfm4D',
+ 'applyxfm4D_in.nii.gz',
+ 'applyxfm4D_ref.nii.gz',
+ join(OUTDIR, 'applyxfm4D_out.nii.gz'),
+ 'matfiles_four_digit',
+ '-interp',
+ 'trilinear',
+ '-fourdigit']
+run(cmd, check=True)
diff --git a/unit_tests/applyxfm4D/feedsRun.nn b/unit_tests/applyxfm4D/feedsRun.nn
new file mode 100755
index 0000000000000000000000000000000000000000..ceb1cb142a51fa4c9e47ee40588e4c5cc8f5c790
--- /dev/null
+++ b/unit_tests/applyxfm4D/feedsRun.nn
@@ -0,0 +1,19 @@
+#!/usr/bin/env fslpython
+"""
+test applyxfm4D nn interp
+"""
+import sys
+from subprocess import run
+from os.path import join
+
+OUTDIR = sys.argv[1]
+cmd = [
+ 'applyxfm4D',
+ 'applyxfm4D_in.nii.gz',
+ 'applyxfm4D_ref.nii.gz',
+ join(OUTDIR, 'applyxfm4D_out.nii.gz'),
+ 'applyxfm4D_mat.mat',
+ '-singlematrix',
+ '-interp',
+ 'nn']
+run(cmd, check=True)
diff --git a/unit_tests/applyxfm4D/feedsRun.sinc b/unit_tests/applyxfm4D/feedsRun.sinc
new file mode 100755
index 0000000000000000000000000000000000000000..0507d82a6ecf8d59d80fd202330b57f535f1082d
--- /dev/null
+++ b/unit_tests/applyxfm4D/feedsRun.sinc
@@ -0,0 +1,19 @@
+#!/usr/bin/env fslpython
+"""
+test applyxfm4D sinc interp
+"""
+import sys
+from subprocess import run
+from os.path import join
+
+OUTDIR = sys.argv[1]
+cmd = [
+ 'applyxfm4D',
+ 'applyxfm4D_in.nii.gz',
+ 'applyxfm4D_ref.nii.gz',
+ join(OUTDIR, 'applyxfm4D_out.nii.gz'),
+ 'applyxfm4D_mat.mat',
+ '-singlematrix',
+ '-interp',
+ 'sinc']
+run(cmd, check=True)
diff --git a/unit_tests/applyxfm4D/feedsRun.singlematrix b/unit_tests/applyxfm4D/feedsRun.singlematrix
new file mode 100755
index 0000000000000000000000000000000000000000..729b7c29fa1589c6536ee6a674a369eefb0048bf
--- /dev/null
+++ b/unit_tests/applyxfm4D/feedsRun.singlematrix
@@ -0,0 +1,19 @@
+#!/usr/bin/env fslpython
+"""
+test applyxfm4D single matrix option
+"""
+import sys
+from subprocess import run
+from os.path import join
+
+OUTDIR = sys.argv[1]
+cmd = [
+ 'applyxfm4D',
+ 'applyxfm4D_in.nii.gz',
+ 'applyxfm4D_ref.nii.gz',
+ join(OUTDIR, 'applyxfm4D_out.nii.gz'),
+ 'applyxfm4D_mat.mat',
+ '-singlematrix',
+ '-interp',
+ 'nn']
+run(cmd, check=True)
diff --git a/unit_tests/applyxfm4D/feedsRun.spline b/unit_tests/applyxfm4D/feedsRun.spline
new file mode 100755
index 0000000000000000000000000000000000000000..fd43e22c04c69996ff95d17067c1c8f20c874b33
--- /dev/null
+++ b/unit_tests/applyxfm4D/feedsRun.spline
@@ -0,0 +1,19 @@
+#!/usr/bin/env fslpython
+"""
+test applyxfm4D spline interp
+"""
+import sys
+from subprocess import run
+from os.path import join
+
+OUTDIR = sys.argv[1]
+cmd = [
+ 'applyxfm4D',
+ 'applyxfm4D_in.nii.gz',
+ 'applyxfm4D_ref.nii.gz',
+ join(OUTDIR, 'applyxfm4D_out.nii.gz'),
+ 'applyxfm4D_mat.mat',
+ '-singlematrix',
+ '-interp',
+ 'spline']
+run(cmd, check=True)
diff --git a/unit_tests/applyxfm4D/feedsRun.transdir b/unit_tests/applyxfm4D/feedsRun.transdir
new file mode 100755
index 0000000000000000000000000000000000000000..d6ee3e847c1b4735c258c8345050f6317c01eb88
--- /dev/null
+++ b/unit_tests/applyxfm4D/feedsRun.transdir
@@ -0,0 +1,18 @@
+#!/usr/bin/env fslpython
+"""
+test applyxfm4D matfile directory option
+"""
+import sys
+from subprocess import run
+from os.path import join
+
+OUTDIR = sys.argv[1]
+cmd = [
+ 'applyxfm4D',
+ 'applyxfm4D_in.nii.gz',
+ 'applyxfm4D_ref.nii.gz',
+ join(OUTDIR, 'applyxfm4D_out.nii.gz'),
+ 'matfiles_five_digit',
+ '-interp',
+ 'trilinear']
+run_result = run(cmd, check=True)
diff --git a/unit_tests/applyxfm4D/feedsRun.trilinear b/unit_tests/applyxfm4D/feedsRun.trilinear
new file mode 100755
index 0000000000000000000000000000000000000000..615dff39584979aad946cdbedda8f733d89cb292
--- /dev/null
+++ b/unit_tests/applyxfm4D/feedsRun.trilinear
@@ -0,0 +1,19 @@
+#!/usr/bin/env fslpython
+"""
+test applyxfm4D trilinear interp
+"""
+import sys
+from subprocess import run
+from os.path import join
+
+OUTDIR = sys.argv[1]
+cmd = [
+ 'applyxfm4D',
+ 'applyxfm4D_in.nii.gz',
+ 'applyxfm4D_ref.nii.gz',
+ join(OUTDIR, 'applyxfm4D_out.nii.gz'),
+ 'applyxfm4D_mat.mat',
+ '-singlematrix',
+ '-interp',
+ 'trilinear']
+run(cmd, check=True)
diff --git a/unit_tests/applyxfm4D/feedsRun.userprefix b/unit_tests/applyxfm4D/feedsRun.userprefix
new file mode 100755
index 0000000000000000000000000000000000000000..32be3f1aab8002cdf456c3456887eb3070788b72
--- /dev/null
+++ b/unit_tests/applyxfm4D/feedsRun.userprefix
@@ -0,0 +1,20 @@
+#!/usr/bin/env fslpython
+"""
+test applyxfm4D matfile directory option with user prefix
+"""
+import sys
+from subprocess import run
+from os.path import join
+
+OUTDIR = sys.argv[1]
+cmd = [
+ 'applyxfm4D',
+ 'applyxfm4D_in.nii.gz',
+ 'applyxfm4D_ref.nii.gz',
+ join(OUTDIR, 'applyxfm4D_out.nii.gz'),
+ 'matfiles_user_prefix',
+ '-interp',
+ 'trilinear',
+ '-userprefix',
+ 'myprefix_']
+run_result = run(cmd, check=True)
diff --git a/unit_tests/applyxfm4D/applyxfm4D_singlematrix/.DS_Store b/unit_tests/applyxfm4D/matfiles_five_digit/.DS_Store
similarity index 100%
rename from unit_tests/applyxfm4D/applyxfm4D_singlematrix/.DS_Store
rename to unit_tests/applyxfm4D/matfiles_five_digit/.DS_Store
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00000 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00000
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00000
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00001 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00001
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00001
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00002 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00002
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00002
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00003 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00003
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00003
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00004 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00004
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00004
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00005 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00005
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00005
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00006 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00006
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00006
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
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+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00007 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00007
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00007
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00008 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00008
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00008
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00009 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00009
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00009
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00010 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00010
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00010
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00011 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00011
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00011
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00012 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00012
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00012
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
+0.0000000000 0.0000000000 1.0000000000 2.0000000000
+0.0000000000 0.0000000000 0.0000000000 1.0000000000
diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00013 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00013
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00013
@@ -0,0 +1,4 @@
+1.0000000000 0.0000000000 0.0000000000 -0.3750000000
+0.0000000000 1.0000000000 0.0000000000 0.8958333450
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diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00014 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00014
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00014
@@ -0,0 +1,4 @@
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diff --git a/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00015 b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00015
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_five_digit/MAT_00015
@@ -0,0 +1,4 @@
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/.DS_Store b/unit_tests/applyxfm4D/matfiles_four_digit/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/unit_tests/applyxfm4D/matfiles_four_digit/.DS_Store differ
diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0000 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0000
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0000
@@ -0,0 +1,4 @@
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0001 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0001
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0001
@@ -0,0 +1,4 @@
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0002 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0002
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0002
@@ -0,0 +1,4 @@
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0003 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0003
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0003
@@ -0,0 +1,4 @@
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0004 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0004
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0004
@@ -0,0 +1,4 @@
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new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
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new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0008 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0008
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
+++ b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0008
@@ -0,0 +1,4 @@
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0009 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0009
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
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@@ -0,0 +1,4 @@
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0010 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0010
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0011 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0011
new file mode 100644
index 0000000000000000000000000000000000000000..8e01b80c78cfc1743d002cb35e1c08c54e055c77
--- /dev/null
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diff --git a/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0012 b/unit_tests/applyxfm4D/matfiles_four_digit/MAT_0012
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