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FIX: Use seconds as time units when converting PARRECHeader to Nifti1Header #931

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Merged
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Jul 13, 2020
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FIX: Use seconds as time units when converting PARRECHeader to Nifti1Header #931

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8333780
FIX: Save TR in seconds in parrec2nii
effigies Jul 6, 2020
7759954
TEST: Verify that header conversion preserves units
effigies Jul 6, 2020
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3 changes: 2 additions & 1 deletion nibabel/parrec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -775,7 +775,8 @@ def as_analyze_map(self):
self.general_info['exam_date'].replace(' ', ''),
self.general_info['protocol_name']))[:80] # max len
is_fmri = (self.general_info['max_dynamics'] > 1)
t = 'msec' if is_fmri else 'unknown'
# PAR/REC uses msec, but in _calc_zooms we convert to sec
t = 'sec' if is_fmri else 'unknown'
xyzt_units = unit_codes['mm'] + unit_codes[t]
return dict(descr=descr, xyzt_units=xyzt_units) # , pixdim=pixdim)

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14 changes: 13 additions & 1 deletion nibabel/tests/test_parrec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
from numpy import array as npa

from .. import load as top_load
from ..nifti1 import Nifti1Image, Nifti1Extension
from ..nifti1 import Nifti1Image, Nifti1Extension, Nifti1Header
from .. import parrec
from ..parrec import (parse_PAR_header, PARRECHeader, PARRECError, vol_numbers,
vol_is_full, PARRECImage, PARRECArrayProxy, exts2pars)
Expand Down Expand Up @@ -549,6 +549,18 @@ def test_epi_params():
assert_almost_equal(epi_hdr.get_zooms()[-1], 2.0)


def test_xyzt_unit_conversion():
# Check conversion to NIfTI-like has sensible units
for par_root in ('T2_-interleaved', 'T2_', 'phantom_EPI_asc_CLEAR_2_1'):
epi_par = pjoin(DATA_PATH, par_root + '.PAR')
with open(epi_par, 'rt') as fobj:
epi_hdr = PARRECHeader.from_fileobj(fobj)
nifti_hdr = Nifti1Header.from_header(epi_hdr)
assert len(nifti_hdr.get_data_shape()) == 4
assert_almost_equal(nifti_hdr.get_zooms()[-1], 2.0)
assert nifti_hdr.get_xyzt_units() == ('mm', 'sec')


def test_truncations():
# Test tests for truncation
par = pjoin(DATA_PATH, 'T2_.PAR')
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