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BF: fix repetition time in PARREC header #692

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BF: fix repetition time in PARREC header #692

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4 changes: 2 additions & 2 deletions nibabel/parrec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -897,11 +897,11 @@ def _calc_zooms(self):
zooms[:2] = self._get_unique_image_prop('pixel spacing')
slice_thickness = self._get_unique_image_prop('slice thickness')
zooms[2] = slice_thickness + slice_gap
# If 4D dynamic scan, convert time from milliseconds to seconds
# If 4D dynamic scan, save repetition time in miliseconds
if len(zooms) > 3 and self.general_info['dyn_scan']:
if len(self.general_info['repetition_time']) > 1:
warnings.warn("multiple TRs found in .PAR file")
zooms[3] = self.general_info['repetition_time'][0] / 1000.
zooms[3] = self.general_info['repetition_time'][0]
return zooms

def get_affine(self, origin='scanner'):
Expand Down
8 changes: 4 additions & 4 deletions nibabel/tests/test_parrec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,7 @@
# We disagree with Philips about the right affine, for the moment, so
# use our own affine as determined from a previous load in nibabel
affine=AN_OLD_AFFINE,
zooms=(3.75, 3.75, 8.0, 2.0),
zooms=(3.75, 3.75, 8.0, 2000.0),
data_summary=dict(
min=0.0,
max=2299.4110643863678,
Expand Down Expand Up @@ -179,7 +179,7 @@ def test_header():
hdr = PARRECHeader(HDR_INFO, HDR_DEFS)
assert_equal(hdr.get_data_shape(), (64, 64, 9, 3))
assert_equal(hdr.get_data_dtype(), np.dtype('<u2'))
assert_equal(hdr.get_zooms(), (3.75, 3.75, 8.0, 2.0))
assert_equal(hdr.get_zooms(), (3.75, 3.75, 8.0, 2000.0))
assert_equal(hdr.get_data_offset(), 0)
si = np.array(
[np.unique(x) for x in hdr.get_data_scaling()]).ravel()
Expand Down Expand Up @@ -548,7 +548,7 @@ def test_epi_params():
with open(epi_par, 'rt') as fobj:
epi_hdr = PARRECHeader.from_fileobj(fobj)
assert_equal(len(epi_hdr.get_data_shape()), 4)
assert_almost_equal(epi_hdr.get_zooms()[-1], 2.0)
assert_almost_equal(epi_hdr.get_zooms()[-1], 2000.0)


def test_truncations():
Expand Down Expand Up @@ -832,7 +832,7 @@ def test_dualTR():
assert_array_equal(dualTR_hdr.general_info['repetition_time'],
expected_TRs)
# zoom on 4th dimensions is the first TR (in seconds)
assert_equal(dualTR_hdr.get_zooms()[3], expected_TRs[0]/1000)
assert_equal(dualTR_hdr.get_zooms()[3], expected_TRs[0])


def test_ADC_map():
Expand Down