From 562dab0f90a110c5a17a72a40660f4c505c0669a Mon Sep 17 00:00:00 2001 From: hstojic Date: Mon, 21 Jan 2019 17:47:45 +0000 Subject: [PATCH 1/2] added flags option to the Level1Design function in SPM interface --- nipype/interfaces/spm/model.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py index 5293346dbb..81cdeb8116 100644 --- a/nipype/interfaces/spm/model.py +++ b/nipype/interfaces/spm/model.py @@ -106,6 +106,7 @@ class Level1DesignInputSpec(SPMCommandInputSpec): desc=('Model serial correlations ' 'AR(1), FAST or none. FAST ' 'is available in SPM12')) + flags = traits.Dict(desc='Additional arguments to the job, e.g. a common SPm operation is to modify the default masking threshold (mthresh)') class Level1DesignOutputSpec(TraitedSpec): @@ -125,6 +126,7 @@ class Level1Design(SPMCommand): >>> level1design.inputs.interscan_interval = 2.5 >>> level1design.inputs.bases = {'hrf':{'derivs': [0,0]}} >>> level1design.inputs.session_info = 'session_info.npz' + >>> level1design.inputs.flags = {'mthresh': 0.4} >>> level1design.run() # doctest: +SKIP """ @@ -151,7 +153,11 @@ def _parse_inputs(self): """validate spm realign options if set to None ignore """ einputs = super(Level1Design, - self)._parse_inputs(skip=('mask_threshold')) + self)._parse_inputs(skip=('mask_threshold', 'flags')) + if isdefined(self.inputs.flags): + einputs[0].update( + {flag: val + for (flag, val) in self.inputs.flags.items()}) for sessinfo in einputs[0]['sess']: sessinfo['scans'] = scans_for_fnames( ensure_list(sessinfo['scans']), keep4d=False) From 1f9f106bc8fecc4c9ebaa538ebf3e9a1ea69595b Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Sat, 23 Feb 2019 11:51:56 +0000 Subject: [PATCH 2/2] Update nipype/interfaces/spm/model.py Co-Authored-By: hstojic --- nipype/interfaces/spm/model.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py index 81cdeb8116..4fb1c51e08 100644 --- a/nipype/interfaces/spm/model.py +++ b/nipype/interfaces/spm/model.py @@ -106,7 +106,9 @@ class Level1DesignInputSpec(SPMCommandInputSpec): desc=('Model serial correlations ' 'AR(1), FAST or none. FAST ' 'is available in SPM12')) - flags = traits.Dict(desc='Additional arguments to the job, e.g. a common SPm operation is to modify the default masking threshold (mthresh)') + flags = traits.Dict( + desc='Additional arguments to the job, e.g., a common SPM operation is to ' + 'modify the default masking threshold (mthresh)') class Level1DesignOutputSpec(TraitedSpec):