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fix: ensure that T2 file gets used to clean surface #1282

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Merged
merged 1 commit into from
Nov 24, 2015
Merged

fix: ensure that T2 file gets used to clean surface #1282

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4 changes: 3 additions & 1 deletion nipype/interfaces/freesurfer/preprocess.py
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Expand Up @@ -609,7 +609,9 @@ class ReconAllInputSpec(CommandLineInputSpec):
T1_files = InputMultiPath(File(exists=True), argstr='-i %s...',
desc='name of T1 file to process')
T2_file = File(exists=True, argstr="-T2 %s", min_ver='5.3.0',
desc='Use a T2 image to refine the cortical surface')
desc='Convert T2 image to orig directory')
use_T2 = traits.Bool(argstr="-T2pial", min_ver='5.3.0',
desc='Use converted T2 to refine the cortical surface')
openmp = traits.Int(argstr="-openmp %d",
desc="Number of processors to use in parallel")
subjects_dir = Directory(exists=True, argstr='-sd %s', hash_files=False,
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3 changes: 3 additions & 0 deletions nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py
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Expand Up @@ -36,6 +36,9 @@ def test_ReconAll_inputs():
),
terminal_output=dict(nohash=True,
),
use_T2=dict(argstr='-T2pial',
min_ver='5.3.0',
),
)
inputs = ReconAll.input_spec()

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2 changes: 1 addition & 1 deletion nipype/interfaces/freesurfer/utils.py
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Expand Up @@ -360,7 +360,7 @@ def _list_outputs(self):
source = self.inputs.source_file
else:
source = self.inputs.source_annot_file

# Some recon-all files don't have a proper extension (e.g. "lh.thickness")
# so we have to account for that here
bad_extensions = [".%s" % e for e in ["area", "mid", "pial", "avg_curv", "curv", "inflated",
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