From 507aafce331a3090b883e9dbcc3475c2d91a208e Mon Sep 17 00:00:00 2001
From: hstojic <hrvoje.stojic@protonmail.com>
Date: Thu, 31 Jan 2019 20:26:35 +0000
Subject: [PATCH 1/3] adding SPM orth argument to the SpecifyModel class
---
nipype/algorithms/modelgen.py | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py
index 9a0984c885..1d58f5de6e 100644
--- a/nipype/algorithms/modelgen.py
+++ b/nipype/algorithms/modelgen.py
@@ -331,8 +331,7 @@ class SpecifyModel(BaseInterface):
- amplitudes : lists of amplitudes for each event. This will be ignored by
SPM's Level1Design.
- The following two (tmod, pmod) will be ignored by any Level1Design class
- other than SPM:
+ The following three (tmod, pmod, orth) will be ignored by any Level1Design class other than SPM:
- tmod : lists of conditions that should be temporally modulated. Should
default to None if not being used.
@@ -340,6 +339,11 @@ class SpecifyModel(BaseInterface):
- name : name of parametric modulator
- param : values of the modulator
- poly : degree of modulation
+ - orth : lists of instructions to orthogonolise parametric regressors or
+ not. Same as in SPM, use 'Yes' to indicate orthogonalisation, and 'No'
+ to explicitly prevent it. Use None for conditions where it is not being
+ used. Note that by default SPM will orthogonalise parametric regressors
+ in the order in which they are entered.
Alternatively, you can provide information through event files.
@@ -369,7 +373,7 @@ class SpecifyModel(BaseInterface):
None])
>>> evs_run3 = Bunch(conditions=['cond1', 'cond2'], onsets=[[20, 120], [80, 160]], \
durations=[[0], [0]], pmod=[Bunch(name=['amp'], poly=[2], param=[[1, 2]]), \
-None])
+None], orth=['No', None])
>>> s.inputs.subject_info = [evs_run2, evs_run3]
"""
@@ -414,6 +418,12 @@ def _generate_standard_design(self,
if hasattr(info, 'tmod') and info.tmod and \
len(info.tmod) > cid:
sessinfo[i]['cond'][cid]['tmod'] = info.tmod[cid]
+
+ if hasattr(info, 'orth') and info.orth:
+ if info.orth[cid] == 'Yes':
+ sessinfo[i]['cond'][cid]['orth'] = 1
+ elif info.orth[cid] == 'No':
+ sessinfo[i]['cond'][cid]['orth'] = 0
if hasattr(info, 'pmod') and info.pmod and \
len(info.pmod) > cid:
From 3d8c80dc02da78a4f25f6d411bb1b9e47987833d Mon Sep 17 00:00:00 2001
From: hstojic <hrvoje.stojic@protonmail.com>
Date: Thu, 21 Feb 2019 12:45:12 +0000
Subject: [PATCH 2/3] removed whitespaces, added ValueError if orth not None
---
nipype/algorithms/modelgen.py | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py
index 1d58f5de6e..05a9193053 100644
--- a/nipype/algorithms/modelgen.py
+++ b/nipype/algorithms/modelgen.py
@@ -339,10 +339,10 @@ class SpecifyModel(BaseInterface):
- name : name of parametric modulator
- param : values of the modulator
- poly : degree of modulation
- - orth : lists of instructions to orthogonolise parametric regressors or
- not. Same as in SPM, use 'Yes' to indicate orthogonalisation, and 'No'
- to explicitly prevent it. Use None for conditions where it is not being
- used. Note that by default SPM will orthogonalise parametric regressors
+ - orth : lists of instructions to orthogonolise parametric regressors or
+ not. Same as in SPM, use 'Yes' to indicate orthogonalisation, and 'No'
+ to explicitly prevent it. Use None for conditions where it is not being
+ used. Note that by default SPM will orthogonalise parametric regressors
in the order in which they are entered.
Alternatively, you can provide information through event files.
@@ -419,11 +419,14 @@ def _generate_standard_design(self,
len(info.tmod) > cid:
sessinfo[i]['cond'][cid]['tmod'] = info.tmod[cid]
- if hasattr(info, 'orth') and info.orth:
+ if hasattr(info, 'orth') and info.orth and\
+ len(info.orth) > cid:
if info.orth[cid] == 'Yes':
sessinfo[i]['cond'][cid]['orth'] = 1
elif info.orth[cid] == 'No':
sessinfo[i]['cond'][cid]['orth'] = 0
+ elif info.orth[cid] is not None:
+ raise ValueError("Unknown orthogonalization option {0}. Must be one of 'Yes', 'No', or None.".format(info.orth[cid]))
if hasattr(info, 'pmod') and info.pmod and \
len(info.pmod) > cid:
From d3ec0aa26dbdf6a5637fe00f8ed7aea18efbaf6d Mon Sep 17 00:00:00 2001
From: hstojic <hrvoje.stojic@protonmail.com>
Date: Sat, 23 Feb 2019 11:37:10 +0000
Subject: [PATCH 3/3] removed trailing whitespaces
---
nipype/algorithms/modelgen.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py
index 05a9193053..3e2e4b9f11 100644
--- a/nipype/algorithms/modelgen.py
+++ b/nipype/algorithms/modelgen.py
@@ -418,7 +418,7 @@ def _generate_standard_design(self,
if hasattr(info, 'tmod') and info.tmod and \
len(info.tmod) > cid:
sessinfo[i]['cond'][cid]['tmod'] = info.tmod[cid]
-
+
if hasattr(info, 'orth') and info.orth and\
len(info.orth) > cid:
if info.orth[cid] == 'Yes':