diff --git a/unit_tests/avwutils/fslcreatehd/feedsRun b/unit_tests/avwutils/fslcreatehd/feedsRun
index 5668155d52780c93842fe4159dfd43b7ceb77eeb..c1ce6e473f26d97aec5552f4107eb2752652d404 100755
--- a/unit_tests/avwutils/fslcreatehd/feedsRun
+++ b/unit_tests/avwutils/fslcreatehd/feedsRun
@@ -1,6 +1,7 @@
#!/usr/bin/env fslpython
import os
+import os.path as op
import sys
import subprocess as sp
@@ -8,6 +9,9 @@ import numpy as np
import nibabel as nib
+THISDIR = op.dirname(__file__)
+
+
# 2=char, 4=short, 8=int, 16=float, 64=double
DTYPE_MAPPING = {
2 : np.uint8,
@@ -17,6 +21,11 @@ DTYPE_MAPPING = {
64 : np.float64
}
+MNI152_2MM_AFFINE = np.array([[-2, 0, 0, 90],
+ [ 0, 2, 0, -126],
+ [ 0, 0, 2, -72],
+ [ 0, 0, 0, 1]])
+
def validate_result(imgfile, expshape, exppixdim, exporigin, expdtype):
@@ -83,6 +92,13 @@ def test_new_file():
args = list(test.split())
imgfile = 'image.nii.gz'
+ try:
+ os.remove(imgfile)
+ except:
+ pass
+
+ print(['fslcreatehd'] + args + [imgfile])
+
sp.run(['fslcreatehd'] + args + [imgfile])
args = [float(a) for a in args]
@@ -175,9 +191,72 @@ def test_existing_file():
os.remove(imgfile)
+def test_new_file_xml():
+ xmlfile = op.join(THISDIR, 'mni2mm.xml')
+ sp.run(['fslcreatehd', xmlfile, 'mni.nii.gz'])
+ img = nib.load('mni.nii.gz')
+
+ assert img.shape == (91, 109, 91)
+ assert img.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
+ assert img.header['intent_code'] == 10
+ assert img.header['intent_p1'] == 20
+ assert img.header['intent_p2'] == 30
+ assert img.header['intent_p3'] == 40
+
+
+def test_existing_file_xml_same_shape():
+ xmlfile = op.join(THISDIR, 'mni2mm.xml')
+ img = create_image((91, 109, 91), (3, 3, 3), (5, 5, 5), np.float32)
+ img.to_filename('image.nii.gz')
+
+ sp.run(['fslcreatehd', xmlfile, 'image.nii.gz'])
+
+ result = nib.load('image.nii.gz')
+
+ assert result.shape == (91, 109, 91)
+ assert result.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
+
+ # bug in FSL<=6.0.4 caused intent codes to not be set
+ assert result.header['intent_code'] == 10
+ assert result.header['intent_p1'] == 20
+ assert result.header['intent_p2'] == 30
+ assert result.header['intent_p3'] == 40
+ assert np.all(result.affine == MNI152_2MM_AFFINE)
+
+ # data should be preserved
+ assert np.all(result.get_fdata() == img.get_fdata())
+
+
+def test_existing_file_xml_different_shape():
+
+ xmlfile = op.join(THISDIR, 'mni2mm.xml')
+ img = create_image((20, 20, 20), (3, 3, 3), (5, 5, 5), np.float32)
+
+ img.to_filename('image.nii.gz')
+
+ sp.run(['fslcreatehd', xmlfile, 'image.nii.gz'])
+
+ result = nib.load('image.nii.gz')
+
+ assert result.shape == (91, 109, 91)
+ assert result.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
+ assert result.header['intent_code'] == 10
+ assert result.header['intent_p1'] == 20
+ assert result.header['intent_p2'] == 30
+ assert result.header['intent_p3'] == 40
+ assert np.all(result.affine == MNI152_2MM_AFFINE)
+
+ # data should be cleared
+ assert np.all(result.get_fdata() == 0)
+
+
def main():
test_new_file()
test_existing_file()
+ test_new_file_xml()
+ test_existing_file_xml_same_shape()
+ test_existing_file_xml_different_shape()
+
if __name__ == '__main__':
sys.exit(main())
diff --git a/unit_tests/avwutils/fslcreatehd/mni2mm.xml b/unit_tests/avwutils/fslcreatehd/mni2mm.xml
new file mode 100644
index 0000000000000000000000000000000000000000..06b8043c942be6a6bec7c11a26aa44a5cb243471
--- /dev/null
+++ b/unit_tests/avwutils/fslcreatehd/mni2mm.xml
@@ -0,0 +1,44 @@
+<nifti_image
+ image_offset = '352'
+ ndim = '3'
+ nx = '91'
+ ny = '109'
+ nz = '91'
+ nt = '1'
+ dx = '2'
+ dy = '2'
+ dz = '2'
+ dt = '1'
+ datatype = '4'
+ nvox = '902629'
+ nbyper = '2'
+ scl_slope = '1'
+ scl_inter = '0'
+ intent_code = '10'
+ intent_p1 = '20'
+ intent_p2 = '30'
+ intent_p3 = '40'
+ intent_name = ''
+ toffset = '0'
+ xyz_units = '2'
+ time_units = '8'
+ freq_dim = '0'
+ phase_dim = '0'
+ slice_dim = '0'
+ descrip = 'FSL5.0'
+ aux_file = ''
+ qform_code = '4'
+ qfac = '-1'
+ quatern_b = '0'
+ quatern_c = '1'
+ quatern_d = '0'
+ qoffset_x = '90'
+ qoffset_y = '-126'
+ qoffset_z = '-72'
+ sform_code = '4'
+ sto_xyz_matrix = '-2 0 0 90 0 2 0 -126 0 0 2 -72 0 0 0 1'
+ slice_code = '0'
+ slice_start = '0'
+ scl_end = '0'
+ scl_duration = '0'
+/>