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ENH: Enable orthogonalization in SPM models via SpecifyModel #2870

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ENH: Enable orthogonalization in SPM models via SpecifyModel #2870

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507aafc
adding SPM orth argument to the SpecifyModel class
hstojic Jan 31, 2019
3d8c80d
removed whitespaces, added ValueError if orth not None
hstojic Feb 21, 2019
d3ec0aa
removed trailing whitespaces
hstojic Feb 23, 2019
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19 changes: 16 additions & 3 deletions nipype/algorithms/modelgen.py
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Original file line number Diff line number Diff line change
Expand Up @@ -331,15 +331,19 @@ 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.
- pmod : list of Bunch corresponding to conditions
- 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.
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can we enable the option where order does not matter? this was the fix in spm12. it's not actually fine to create orthogonalization options where order is important.

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it's possible this is the default, in which case the sentence above should be fixed.

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default == independent orthogonalization

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As far as I know in SPM12 order still matters bcs orthogonalisation is done with respect to regressors entered previously. SPM8 was doing orthogonalisation automatically and switching it off required a hacky solution, while SPM12 does it by default, but now you can instruct it not to do it. I know this type of orthogonalisation is not necessarily OK, here I am simply implementing this option to switch it off.

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according to this:

problem here: https://www.youtube.com/watch?v=HA_yjX868Ro&feature=youtu.be&t=915
spm12 reference here: https://youtu.be/HA_yjX868Ro?t=1027

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@gllmflndn - is there a way to enable this programmatically?


Alternatively, you can provide information through event files.

Expand Down Expand Up @@ -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]

"""
Expand Down Expand Up @@ -414,6 +418,15 @@ 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':
sessinfo[i]['cond'][cid]['orth'] = 1
elif info.orth[cid] == 'No':
sessinfo[i]['cond'][cid]['orth'] = 0
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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:
Expand Down