8000 Issue 3553 add mvecs to dcm2niix by pvelasco · Pull Request #3554 · nipy/nipype · GitHub
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Issue 3553 add mvecs to dcm2niix #3554

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Merged
merged 6 commits into from
Jul 5, 2023
Merged

Issue 3553 add mvecs to dcm2niix #3554

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fd4b8bd
ENH: Dcm2niix - add mvec output
pvelasco Mar 23, 2023
cd3c20f
NEW: add pvelasco to .zenodo.json
pvelasco Mar 23, 2023
09a44f4
LINT: Black edits
pvelasco Mar 24, 2023
4195b9e
Merge pull request #1 from pvelasco/black-formatting
pvelasco Mar 24, 2023
f9ca616
Merge branch 'master' into issue-3553_add_mvecs_to_Dcm2niix
effigies Jul 5, 2023
42f3efd
Merge branch 'master' into issue-3553_add_mvecs_to_Dcm2niix
effigies Jul 5, 2023
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ENH: Dcm2niix - add mvec output
  • Loading branch information
@pvelasco
pvelasco committed Mar 23, 2023
commit fd4b8bdb47eda74011ffceeccb5fcc5ea15547d0
12 changes: 9 additions & 3 deletions nipype/interfaces/dcm2nii.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,8 @@ class Dcm2nii(CommandLine):
>>> converter.inputs.gzip_output = True
>>> converter.inputs.output_dir = '.'
>>> converter.cmdline # doctest: +ELLIPSIS
'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'"""
'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'
"""

input_spec = Dcm2niiInputSpec
output_spec = Dcm2niiOutputSpec
Expand Down Expand Up @@ -374,6 +375,7 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
class Dcm2niixOutputSpec(TraitedSpec):
converted_files = OutputMultiPath(File(exists=True))
bvecs = OutputMultiPath(File(exists=True))
mvecs = OutputMultiPath(File(exists=True))
bvals = OutputMultiPath(File(exists=True))
bids = OutputMultiPath(File(exists=True))

Expand Down Expand Up @@ -456,8 +458,8 @@ def _parse_stdout(self, stdout):
return filenames

def _parse_files(self, filenames):
outfiles, bvals, bvecs, bids = [], [], [], []
outtypes = [".bval", ".bvec", ".json", ".txt"]
outfiles, bvals, bvecs, mvecs, bids = [], [], [], [], []
outtypes = [".bval", ".bvec", ".mvec", ".json", ".txt"]
if self.inputs.to_nrrd:
outtypes += [".nrrd", ".nhdr", ".raw.gz"]
else:
Expand All @@ -477,10 +479,13 @@ def _parse_files(self, filenames):
bvals.append(fl)
elif fl.endswith(".bvec"):
bvecs.append(fl)
elif fl.endswith(".mvec"):
mvecs.append(fl)
elif fl.endswith(".json") or fl.endswith(".txt"):
bids.append(fl)
self.output_files = outfiles
self.bvecs = bvecs
self.mvecs = mvecs
self.bvals = bvals
self.bids = bids

Expand All @@ -489,6 +494,7 @@ def _list_outputs(self):
outputs["converted_files"] = self.output_files
outputs["bvecs"] = self.bvecs
outputs["bvals"] = self.bvals
outputs["mvecs"] = self.mvecs
outputs["bids"] = self.bids
return outputs

Expand Down
1 change: 1 addition & 0 deletions nipype/interfaces/tests/test_auto_Dcm2niix.py
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Expand Up @@ -95,6 +95,7 @@ def test_Dcm2niix_outputs():
bvals=dict(),
bvecs=dict(),
converted_files=dict(),
mvecs=dict(),
)
outputs = Dcm2niix.output_spec()

Expand Down
0