From 9f8f12606bae53cafddcf659e95a6c99de3dbdac Mon Sep 17 00:00:00 2001 From: achetverikov Date: Thu, 18 Jan 2018 12:53:48 +0100 Subject: [PATCH 1/6] Fixed a small bug in label2annot fill_thresh specs (should be %f instead of %.f) --- nipype/interfaces/freesurfer/model.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py index e2eba23196..fe137a3b62 100644 --- a/nipype/interfaces/freesurfer/model.py +++ b/nipype/interfaces/freesurfer/model.py @@ -917,7 +917,7 @@ class Label2VolInputSpec(FSTraitedSpec): desc='set R=I') invert_mtx = traits.Bool(argstr='--invertmtx', desc='Invert the registration matrix') - fill_thresh = traits.Range(0., 1., argstr='--fillthresh %.f', + fill_thresh = traits.Range(0., 1., argstr='--fillthresh %f', desc='thresh : between 0 and 1') label_voxel_volume = traits.Float(argstr='--labvoxvol %f', desc='volume of each label point (def 1mm3)') From 7723d30405d562b49e8c722ce71ee2a27a5b55cb Mon Sep 17 00:00:00 2001 From: achetverikov Date: Fri, 23 Feb 2018 09:53:17 +0100 Subject: [PATCH 2/6] TEST: make specs --- nipype/interfaces/freesurfer/tests/test_auto_Binarize.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py | 2 +- .../freesurfer/tests/test_auto_MRISPreprocReconAll.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_SegStats.py | 2 +- .../interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py | 2 +- .../interfaces/freesurfer/tests/test_auto_SphericalAverage.py | 2 +- 13 files changed, 13 insertions(+), 13 deletions(-) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index adac7e5ad8..d1dcff9155 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import Binarize +from ..model_bkp import Binarize def test_Binarize_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index efa08400f3..fc42b062be 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import Concatenate +from ..model_bkp import Concatenate def test_Concatenate_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index b310eded87..93c3b86cc4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import GLMFit +from ..model_bkp import GLMFit def test_GLMFit_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py index 1e94061567..d56802be78 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import Label2Annot +from ..model_bkp import Label2Annot def test_Label2Annot_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py index 581a5d8898..d3dd46b5f4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import Label2Label +from ..model_bkp import Label2Label def test_Label2Label_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index 971bc20062..d96d0886b1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import Label2Vol +from ..model_bkp import Label2Vol def test_Label2Vol_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index ce68c41056..697c65e1df 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import MRISPreproc +from ..model_bkp import MRISPreproc def test_MRISPreproc_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py index 677d9dda5a..209b4f8d72 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import MRISPreprocReconAll +from ..model_bkp import MRISPreprocReconAll def test_MRISPreprocReconAll_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index 6c978254a5..bc3ac759e6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import MS_LDA +from ..model_bkp import MS_LDA def test_MS_LDA_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index c8b6422dd0..95767c7a41 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import OneSampleTTest +from ..model_bkp import OneSampleTTest def test_OneSampleTTest_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index 4dbbf24d3a..5fb5da0f6a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import SegStats +from ..model_bkp import SegStats def test_SegStats_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index f528748743..3b8a78fb91 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import SegStatsReconAll +from ..model_bkp import SegStatsReconAll def test_SegStatsReconAll_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py index 7942f5250a..08751365ca 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model import SphericalAverage +from ..model_bkp import SphericalAverage def test_SphericalAverage_inputs(): From dfb331112fc4264f2f5492a742ae88b726bd3784 Mon Sep 17 00:00:00 2001 From: achetverikov Date: Fri, 23 Feb 2018 16:24:25 +0100 Subject: [PATCH 3/6] TEST: make specs --- nipype/interfaces/freesurfer/tests/test_auto_Binarize.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py | 4 ++-- nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py | 2 +- .../freesurfer/tests/test_auto_MRISPreprocReconAll.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py | 2 +- .../interfaces/freesurfer/tests/test_auto_OneSampleTTest.py | 2 +- nipype/interfaces/freesurfer/tests/test_auto_SegStats.py | 2 +- .../interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py | 2 +- .../interfaces/freesurfer/tests/test_auto_SphericalAverage.py | 2 +- 13 files changed, 14 insertions(+), 14 deletions(-) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index d1dcff9155..adac7e5ad8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import Binarize +from ..model import Binarize def test_Binarize_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index fc42b062be..efa08400f3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import Concatenate +from ..model import Concatenate def test_Concatenate_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index 93c3b86cc4..b310eded87 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import GLMFit +from ..model import GLMFit def test_GLMFit_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py index d56802be78..1e94061567 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import Label2Annot +from ..model import Label2Annot def test_Label2Annot_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py index d3dd46b5f4..581a5d8898 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import Label2Label +from ..model import Label2Label def test_Label2Label_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index d96d0886b1..53dbbd5152 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import Label2Vol +from ..model import Label2Vol def test_Label2Vol_inputs(): @@ -22,7 +22,7 @@ def test_Label2Vol_inputs(): nohash=True, usedefault=True, ), - fill_thresh=dict(argstr='--fillthresh %.f', ), + fill_thresh=dict(argstr='--fillthresh %f', ), hemi=dict(argstr='--hemi %s', ), identity=dict( argstr='--identity', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index 697c65e1df..ce68c41056 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import MRISPreproc +from ..model import MRISPreproc def test_MRISPreproc_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py index 209b4f8d72..677d9dda5a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import MRISPreprocReconAll +from ..model import MRISPreprocReconAll def test_MRISPreprocReconAll_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index bc3ac759e6..6c978254a5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import MS_LDA +from ..model import MS_LDA def test_MS_LDA_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index 95767c7a41..c8b6422dd0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import OneSampleTTest +from ..model import OneSampleTTest def test_OneSampleTTest_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index 5fb5da0f6a..4dbbf24d3a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import SegStats +from ..model import SegStats def test_SegStats_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index 3b8a78fb91..f528748743 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import SegStatsReconAll +from ..model import SegStatsReconAll def test_SegStatsReconAll_inputs(): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py index 08751365ca..7942f5250a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..model_bkp import SphericalAverage +from ..model import SphericalAverage def test_SphericalAverage_inputs(): From 5c7a4467d55996a7050114fe902f007a887fd251 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 23 Feb 2018 10:26:37 -0500 Subject: [PATCH 4/6] STY: Whitespace [skip ci] --- nipype/interfaces/freesurfer/model.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py index dfd1e1f6ba..db5dd9a0eb 100644 --- a/nipype/interfaces/freesurfer/model.py +++ b/nipype/interfaces/freesurfer/model.py @@ -1170,6 +1170,7 @@ class Label2VolInputSpec(FSTraitedSpec): argstr='--native-vox2ras', desc='use native vox2ras xform instead of tkregister-style') + class Label2VolOutputSpec(TraitedSpec): vol_label_file = File(exists=True, desc='output volume') From cf5821b2466ab4afbc10a7eedfe936cb801495e7 Mon Sep 17 00:00:00 2001 From: achetverikov Date: Sat, 24 Feb 2018 10:14:34 +0100 Subject: [PATCH 5/6] TEST: make specs --- nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index 53dbbd5152..80747b44ef 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -22,7 +22,7 @@ def test_Label2Vol_inputs(): nohash=True, usedefault=True, ), - fill_thresh=dict(argstr='--fillthresh %f', ), + fill_thresh=dict(argstr='--fillthresh %g', ), hemi=dict(argstr='--hemi %s', ), identity=dict( argstr='--identity', From 03756c3cac64ae4b4cd590dfb0f74a85e75b6655 Mon Sep 17 00:00:00 2001 From: achetverikov Date: Sat, 24 Feb 2018 10:19:10 +0100 Subject: [PATCH 6/6] fix for Label2Annot example command line & change %.f to %g in fillthresh parameter --- nipype/interfaces/freesurfer/model.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py index dfd1e1f6ba..44f9a2ee96 100644 --- a/nipype/interfaces/freesurfer/model.py +++ b/nipype/interfaces/freesurfer/model.py @@ -1144,7 +1144,7 @@ class Label2VolInputSpec(FSTraitedSpec): invert_mtx = traits.Bool( argstr='--invertmtx', desc='Invert the registration matrix') fill_thresh = traits.Range( - 0., 1., argstr='--fillthresh %f', desc='thresh : between 0 and 1') + 0., 1., argstr='--fillthresh %g', desc='thresh : between 0 and 1') label_voxel_volume = traits.Float( argstr='--labvoxvol %f', desc='volume of each label point (def 1mm3)') proj = traits.Tuple( @@ -1182,7 +1182,7 @@ class Label2Vol(FSCommand): >>> binvol = Label2Vol(label_file='cortex.label', template_file='structural.nii', reg_file='register.dat', fill_thresh=0.5, vol_label_file='foo_out.nii') >>> binvol.cmdline - 'mri_label2vol --fillthresh 0 --label cortex.label --reg register.dat --temp structural.nii --o foo_out.nii' + 'mri_label2vol --fillthresh 0.5 --label cortex.label --reg register.dat --temp structural.nii --o foo_out.nii' """