From c9e1d2664fb7269563d0aa6fe10d48832b05526d Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Sun, 14 Jan 2018 11:56:41 -0800 Subject: [PATCH 1/4] Fix 3dFWHMx outputs --- nipype/interfaces/afni/utils.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index 8ddc340858..bd6c8cc517 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -1315,15 +1315,20 @@ def _list_outputs(self): outputs['out_detrend'] = Undefined sout = np.loadtxt(outputs['out_file']) #pylint: disable=E1101 + + # handle newer versions of AFNI + if sout.size == 8: + outputs['fwhm'] = tuple(sout[0,:]) + else: + outputs['fwhm'] = tuple(sout) + if self._acf: outputs['acf_param'] = tuple(sout[1]) - sout = tuple(sout[0]) outputs['out_acf'] = op.abspath('3dFWHMx.1D') if isinstance(self.inputs.acf, (str, bytes)): outputs['out_acf'] = op.abspath(self.inputs.acf) - outputs['fwhm'] = tuple(sout) return outputs From 7c20a7b9226f2a8da8c25076c4e15abaf847a0c8 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Tue, 16 Jan 2018 15:38:59 -0600 Subject: [PATCH 2/4] address review and add changelog --- CHANGES | 1 + nipype/interfaces/afni/utils.py | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGES b/CHANGES index c69b13e672..55bfaa8fa6 100644 --- a/CHANGES +++ b/CHANGES @@ -1,6 +1,7 @@ Upcoming release (0.14.1) ================ +* FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (https://github.com/nipy/nipype/pull/2373) * FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369) * MAINT: Cleaning / simplify ``Node`` (https://github.com/nipy/nipype/pull/#2325) diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index bd6c8cc517..6b59557493 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -1318,11 +1318,12 @@ def _list_outputs(self): # handle newer versions of AFNI if sout.size == 8: - outputs['fwhm'] = tuple(sout[0,:]) + outputs['fwhm'] = tuple(sout[0, :]) else: outputs['fwhm'] = tuple(sout) if self._acf: + assert sout.size == 8, "Wrong number of elements in %s"%str(sout) outputs['acf_param'] = tuple(sout[1]) outputs['out_acf'] = op.abspath('3dFWHMx.1D') From e2d3135f64f199639aaca29170fa38ec9fa2857a Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Tue, 16 Jan 2018 16:14:13 -0600 Subject: [PATCH 3/4] formatting --- CHANGES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGES b/CHANGES index 55bfaa8fa6..933b22cb25 100644 --- a/CHANGES +++ b/CHANGES @@ -1,5 +1,5 @@ Upcoming release (0.14.1) -================ +========================= * FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (https://github.com/nipy/nipype/pull/2373) * FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369) From 5c8e170db8b0c942194d8147af6f4c7da6552c39 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Tue, 16 Jan 2018 16:46:56 -0600 Subject: [PATCH 4/4] pep --- nipype/interfaces/afni/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index 6b59557493..5b5dc79d7f 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -1323,7 +1323,7 @@ def _list_outputs(self): outputs['fwhm'] = tuple(sout) if self._acf: - assert sout.size == 8, "Wrong number of elements in %s"%str(sout) + assert sout.size == 8, "Wrong number of elements in %s" % str(sout) outputs['acf_param'] = tuple(sout[1]) outputs['out_acf'] = op.abspath('3dFWHMx.1D')