diff --git a/unit_tests/applyxfm4D/applyxfm4D_fail/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_fail/feedsInputs
new file mode 100644
index 0000000000000000000000000000000000000000..7782318789d7b5b47150a948cb29e67c3d5a16fc
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_fail/feedsInputs
@@ -0,0 +1 @@
+unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_fail/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_fail/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..e9301f09c75e74ef4f74a70ad1b40956c1b970d8
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_fail/feedsRun
@@ -0,0 +1,33 @@
+#!/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
new file mode 100644
index 0000000000000000000000000000000000000000..7782318789d7b5b47150a948cb29e67c3d5a16fc
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsInputs
@@ -0,0 +1 @@
+unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..51fac7fb48ab8987695a9a49bd1751b99567f8d5
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsRun
@@ -0,0 +1,34 @@
+#!/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_nn/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_nn/feedsInputs
new file mode 100644
index 0000000000000000000000000000000000000000..7782318789d7b5b47150a948cb29e67c3d5a16fc
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_nn/feedsInputs
@@ -0,0 +1 @@
+unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_nn/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_nn/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..20073bd4c50763b30b752c75a15aaa2bfcb255ee
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_nn/feedsRun
@@ -0,0 +1,33 @@
+#!/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_sinc/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsInputs
new file mode 100644
index 0000000000000000000000000000000000000000..7782318789d7b5b47150a948cb29e67c3d5a16fc
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsInputs
@@ -0,0 +1 @@
+unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..008de98efde7b929efb7719607ae0dfc40506fde
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_sinc/feedsRun
@@ -0,0 +1,33 @@
+#!/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/.DS_Store b/unit_tests/applyxfm4D/applyxfm4D_singlematrix/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/unit_tests/applyxfm4D/applyxfm4D_singlematrix/.DS_Store differ
diff --git a/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsInputs b/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsInputs
new file mode 100644
index 0000000000000000000000000000000000000000..7782318789d7b5b47150a948cb29e67c3d5a16fc
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsInputs
@@ -0,0 +1 @@
+unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..76ce73949b80f3787a5c5ae7a10f39f5f6ad2058
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsRun
@@ -0,0 +1,34 @@
+#!/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
new file mode 100644
index 0000000000000000000000000000000000000000..7782318789d7b5b47150a948cb29e67c3d5a16fc
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_spline/feedsInputs
@@ -0,0 +1 @@
+unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_spline/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_spline/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..c9d20466560a1a6e664a5bb4d6225f8836725ba5
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_spline/feedsRun
@@ -0,0 +1,33 @@
+#!/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
new file mode 100644
index 0000000000000000000000000000000000000000..7782318789d7b5b47150a948cb29e67c3d5a16fc
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsInputs
@@ -0,0 +1 @@
+unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..69428e8fdb0a556c3786c710e9b7288df617f8d1
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_transdir/feedsRun
@@ -0,0 +1,33 @@
+#!/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
new file mode 100644
index 0000000000000000000000000000000000000000..7782318789d7b5b47150a948cb29e67c3d5a16fc
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsInputs
@@ -0,0 +1 @@
+unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..285e95ff6bc4004a3da4d654471a7c86a58ea0fd
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsRun
@@ -0,0 +1,33 @@
+#!/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
new file mode 100644
index 0000000000000000000000000000000000000000..7782318789d7b5b47150a948cb29e67c3d5a16fc
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsInputs
@@ -0,0 +1 @@
+unit_tests/applyxfm4D
diff --git a/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsRun b/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..1679e821b791be1e28eb3b995af13b2d0ccd1c9b
--- /dev/null
+++ b/unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsRun
@@ -0,0 +1,35 @@
+#!/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()