From aaa09f487ed924ddddc2f702c91cec548e807480 Mon Sep 17 00:00:00 2001 From: Chris Filo Gorgolewski Date: Tue, 8 Sep 2015 08:00:38 -0700 Subject: [PATCH 1/4] fixed epireg when there are no fieldmaps --- nipype/interfaces/fsl/epi.py | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py index 7d2784196b..05f73846d2 100644 --- a/nipype/interfaces/fsl/epi.py +++ b/nipype/interfaces/fsl/epi.py @@ -656,16 +656,17 @@ def _list_outputs(self): self.inputs.out_base + '.nii.gz') outputs['out_1vol'] = os.path.join(os.getcwd(), self.inputs.out_base + '_1vol.nii.gz') - outputs['fmap2str_mat'] = os.path.join(os.getcwd(), - self.inputs.out_base + '_fieldmap2str.mat') - outputs['fmap2epi_mat'] = os.path.join(os.getcwd(), - self.inputs.out_base + '_fieldmaprads2epi.mat') - outputs['fmap_epi'] = os.path.join(os.getcwd(), - self.inputs.out_base + '_fieldmaprads2epi.nii.gz') - outputs['fmap_str'] = os.path.join(os.getcwd(), - self.inputs.out_base + '_fieldmaprads2str.nii.gz') - outputs['fmapmag_str'] = os.path.join(os.getcwd(), - self.inputs.out_base + '_fieldmap2str.nii.gz') + if not (isdefined(self.inputs.no_fmapreg) and self.inputs.no_fmapreg): + outputs['fmap2str_mat'] = os.path.join(os.getcwd(), + self.inputs.out_base + '_fieldmap2str.mat') + outputs['fmap2epi_mat'] = os.path.join(os.getcwd(), + self.inputs.out_base + '_fieldmaprads2epi.mat') + outputs['fmap_epi'] = os.path.join(os.getcwd(), + self.inputs.out_base + '_fieldmaprads2epi.nii.gz') + outputs['fmap_str'] = os.path.join(os.getcwd(), + self.inputs.out_base + '_fieldmaprads2str.nii.gz') + outputs['fmapmag_str'] = os.path.join(os.getcwd(), + self.inputs.out_base + '_fieldmap2str.nii.gz') outputs['epi2str_inv'] = os.path.join(os.getcwd(), self.inputs.out_base + '_inv.mat') outputs['epi2str_mat'] = os.path.join(os.getcwd(), From 14591a669a0a0bb0b50c21c0f744e5fce3b2c746 Mon Sep 17 00:00:00 2001 From: Chris Filo Gorgolewski Date: Tue, 8 Sep 2015 09:42:05 -0700 Subject: [PATCH 2/4] skip two more files --- nipype/interfaces/fsl/epi.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py index 05f73846d2..796aa95663 100644 --- a/nipype/interfaces/fsl/epi.py +++ b/nipype/interfaces/fsl/epi.py @@ -667,14 +667,14 @@ def _list_outputs(self): self.inputs.out_base + '_fieldmaprads2str.nii.gz') outputs['fmapmag_str'] = os.path.join(os.getcwd(), self.inputs.out_base + '_fieldmap2str.nii.gz') + outputs['shiftmap'] = os.path.join(os.getcwd(), + self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz') + outputs['fullwarp'] = os.path.join(os.getcwd(), + self.inputs.out_base + '_warp.nii.gz') outputs['epi2str_inv'] = os.path.join(os.getcwd(), self.inputs.out_base + '_inv.mat') outputs['epi2str_mat'] = os.path.join(os.getcwd(), self.inputs.out_base + '.mat') - outputs['shiftmap'] = os.path.join(os.getcwd(), - self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz') - outputs['fullwarp'] = os.path.join(os.getcwd(), - self.inputs.out_base + '_warp.nii.gz') outputs['wmedge'] = os.path.join(os.getcwd(), self.inputs.out_base + '_fast_wmedge.nii.gz') outputs['wmseg'] = os.path.join(os.getcwd(), From 7d1bb137cc1a87392884693cadec1971e3e57483 Mon Sep 17 00:00:00 2001 From: Chris Filo Gorgolewski Date: Tue, 8 Sep 2015 10:36:23 -0700 Subject: [PATCH 3/4] more precise if --- nipype/interfaces/fsl/epi.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py index 796aa95663..78dbe41de9 100644 --- a/nipype/interfaces/fsl/epi.py +++ b/nipype/interfaces/fsl/epi.py @@ -656,7 +656,7 @@ def _list_outputs(self): self.inputs.out_base + '.nii.gz') outputs['out_1vol'] = os.path.join(os.getcwd(), self.inputs.out_base + '_1vol.nii.gz') - if not (isdefined(self.inputs.no_fmapreg) and self.inputs.no_fmapreg): + if not (isdefined(self.inputs.no_fmapreg) and self.inputs.no_fmapreg) or not isdefined(self.inputs.fmap): outputs['fmap2str_mat'] = os.path.join(os.getcwd(), self.inputs.out_base + '_fieldmap2str.mat') outputs['fmap2epi_mat'] = os.path.join(os.getcwd(), From 32923caef25399ddea6d93fd93d3c4000e6201f6 Mon Sep 17 00:00:00 2001 From: Chris Filo Gorgolewski Date: Tue, 8 Sep 2015 20:48:20 -0700 Subject: [PATCH 4/4] make more conditional outputs --- nipype/interfaces/fsl/epi.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py index 78dbe41de9..de5bfb68a6 100644 --- a/nipype/interfaces/fsl/epi.py +++ b/nipype/interfaces/fsl/epi.py @@ -654,9 +654,9 @@ def _list_outputs(self): outputs = self.output_spec().get() outputs['out_file'] = os.path.join(os.getcwd(), self.inputs.out_base + '.nii.gz') - outputs['out_1vol'] = os.path.join(os.getcwd(), + if not (isdefined(self.inputs.no_fmapreg) and self.inputs.no_fmapreg) and isdefined(self.inputs.fmap): + outputs['out_1vol'] = os.path.join(os.getcwd(), self.inputs.out_base + '_1vol.nii.gz') - if not (isdefined(self.inputs.no_fmapreg) and self.inputs.no_fmapreg) or not isdefined(self.inputs.fmap): outputs['fmap2str_mat'] = os.path.join(os.getcwd(), self.inputs.out_base + '_fieldmap2str.mat') outputs['fmap2epi_mat'] = os.path.join(os.getcwd(), @@ -664,15 +664,16 @@ def _list_outputs(self): outputs['fmap_epi'] = os.path.join(os.getcwd(), self.inputs.out_base + '_fieldmaprads2epi.nii.gz') outputs['fmap_str'] = os.path.join(os.getcwd(), - self.inputs.out_base + '_fieldmaprads2str.nii.gz') + self.inputs.out_base + '_fieldmaprads2str.ni `i.gz') outputs['fmapmag_str'] = os.path.join(os.getcwd(), self.inputs.out_base + '_fieldmap2str.nii.gz') outputs['shiftmap'] = os.path.join(os.getcwd(), self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz') outputs['fullwarp'] = os.path.join(os.getcwd(), self.inputs.out_base + '_warp.nii.gz') - outputs['epi2str_inv'] = os.path.join(os.getcwd(), + outputs['epi2str_inv'] = os.path.join(os.getcwd(), self.inputs.out_base + '_inv.mat') + outputs['epi2str_mat'] = os.path.join(os.getcwd(), self.inputs.out_base + '.mat') outputs['wmedge'] = os.path.join(os.getcwd(),