From 92538b95be0e314c74f2588e8175dee26bdcbfee Mon Sep 17 00:00:00 2001 From: Aaron Mattfeld Date: Thu, 17 Sep 2015 23:10:43 -0400 Subject: [PATCH 1/5] Added grad_dev file to inputspec --- nipype/interfaces/fsl/dti.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index 163b2cff36..f26a49cc9c 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -263,6 +263,7 @@ class BEDPOSTX5InputSpec(FSLXCommandInputSpec): usedefault=True, position=1, argstr='%s') gradnonlin = traits.Bool(False, argstr='-g', desc=('consider gradient ' 'nonlinearities, default off')) + grad_dev = File(exists=True, desc='grad_dev file, if gradnonlin, -g is True') use_gpu = traits.Bool(False, desc='Use the GPU version of bedpostx') @@ -346,6 +347,9 @@ def _run_interface(self, runtime): os.path.join(subjectdir, 'bvals')) copyfile(self.inputs.bvecs, os.path.join(subjectdir, 'bvecs')) + _, _, ext = split_filename(self.inputs.grad_dev) + copyfile(self.inputs.grad_dev, + os.path.join(subjectdir, 'grad_dev' + ext)) retval = super(BEDPOSTX5, self)._run_interface(runtime) From 6328903a43eff0e0a615a5f988e350e7323d37eb Mon Sep 17 00:00:00 2001 From: Aaron Mattfeld Date: Fri, 3 Jun 2016 11:54:48 -0400 Subject: [PATCH 2/5] changing spacing back for bedpostx5 gradnonlin inputspec --- nipype/interfaces/fsl/dti.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index a8ad697430..ded847db5e 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -264,7 +264,7 @@ class BEDPOSTX5InputSpec(FSLXCommandInputSpec): out_dir = Directory('bedpostx', mandatory=True, desc='output directory', usedefault=True, position=1, argstr='%s') gradnonlin = traits.Bool(False, argstr='-g', desc=('consider gradient ' - 'nonlinearities, default off')) + 'nonlinearities, default off')) grad_dev = File(exists=True, desc='grad_dev file, if gradnonlin, -g is True') use_gpu = traits.Bool(False, desc='Use the GPU version of bedpostx') From cf77312aec3c8f336d336890479d3fe7d77c4941 Mon Sep 17 00:00:00 2001 From: Aaron Mattfeld Date: Fri, 3 Jun 2016 16:15:39 -0400 Subject: [PATCH 3/5] update CHANGES --- CHANGES | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGES b/CHANGES index 9ab6f15402..b02e7f2b28 100644 --- a/CHANGES +++ b/CHANGES @@ -1,6 +1,7 @@ Release 0.12.0-rc1 (April 20, 2016) ============ +* ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493) * ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372) * ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435) * ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422) From ed90d8a84d8bd687f85de6cb15802d58274d8212 Mon Sep 17 00:00:00 2001 From: Aaron Mattfeld Date: Mon, 6 Jun 2016 10:44:49 -0400 Subject: [PATCH 4/5] update for when grad_dev is not defined --- nipype/interfaces/fsl/dti.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index ded847db5e..eda1e667f3 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -349,9 +349,10 @@ def _run_interface(self, runtime): os.path.join(subjectdir, 'bvals')) copyfile(self.inputs.bvecs, os.path.join(subjectdir, 'bvecs')) - _, _, ext = split_filename(self.inputs.grad_dev) - copyfile(self.inputs.grad_dev, - os.path.join(subjectdir, 'grad_dev' + ext)) + if isdefined(self.inputs.grad_dev): + _, _, ext = split_filename(self.inputs.grad_dev) + copyfile(self.inputs.grad_dev, + os.path.join(subjectdir, 'grad_dev' + ext)) retval = super(BEDPOSTX5, self)._run_interface(runtime) From c33d0ec9f62cde5b84df10d768408bdc19dc7ecb Mon Sep 17 00:00:00 2001 From: Aaron Mattfeld Date: Mon, 6 Jun 2016 10:47:22 -0400 Subject: [PATCH 5/5] updated test_auto_BEDPOSTX5 with grad_dev input --- nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index 48f229eabd..9b02366022 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -36,6 +36,7 @@ def test_BEDPOSTX5_inputs(): ), fudge=dict(argstr='-w %d', ), + grad_dev=dict(), gradnonlin=dict(argstr='-g', ), ignore_exception=dict(nohash=True,