ENH: Enable orthogonalization in SPM models via SpecifyModel #2870

hstojic · 2019-01-31T20:36:08Z

Summary

SPM 12 has an option to switch off the default orthogonolisation of parametric regressors, but it seems that option cannot be set from Nipype - I implemented it here with simple few lines, supplying orth argument as an additional input in the sessioninfo object. Updated the example and function description.

See discussion in issue #2811

Acknowledgment

I acknowledge that this contribution will be available under the Apache 2 license.

codecov-io · 2019-02-04T13:59:41Z

Codecov Report

Merging #2870 into master will decrease coverage by 0.69%.
The diff coverage is 20%.

@@            Coverage Diff            @@
##           master    #2870     +/-   ##
=========================================
- Coverage   67.49%   66.79%   -0.7%     
=========================================
  Files         342      342             
  Lines       43562    43567      +5     
  Branches     5422     5425      +3     
=========================================
- Hits        29402    29101    -301     
- Misses      13458    13723    +265     
- Partials      702      743     +41

Flag	Coverage Δ
#smoketests	`48.64% <20%> (-1.85%)`	⬇️
#unittests	`64.88% <0%> (-0.04%)`	⬇️

Impacted Files	Coverage Δ
nipype/algorithms/modelgen.py	`59.27% <20%> (-4.09%)`	⬇️
nipype/algorithms/rapidart.py	`35% <0%> (-29.42%)`	⬇️
nipype/interfaces/spm/base.py	`68.64% <0%> (-18.49%)`	⬇️
nipype/interfaces/fsl/model.py	`75.3% <0%> (-5.32%)`	⬇️
nipype/interfaces/spm/preprocess.py	`52.88% <0%> (-4.15%)`	⬇️
nipype/pipeline/plugins/legacymultiproc.py	`61.5% <0%> (-3.5%)`	⬇️
nipype/utils/misc.py	`65.43% <0%> (-1.24%)`	⬇️
nipype/pipeline/engine/workflows.py	`77.77% <0%> (-1.18%)`	⬇️
nipype/interfaces/io.py	`54.36% <0%> (-0.71%)`	⬇️
... and 4 more

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codecov-io · 2019-02-04T13:59:44Z

Codecov Report

Merging #2870 into master will decrease coverage by 1.73%.
The diff coverage is 0%.

@@            Coverage Diff             @@
##           master    #2870      +/-   ##
==========================================
- Coverage   67.49%   65.76%   -1.74%     
==========================================
  Files         342      343       +1     
  Lines       43562    44117     +555     
  Branches     5422     5607     +185     
==========================================
- Hits        29402    29013     -389     
- Misses      13458    14208     +750     
- Partials      702      896     +194

Flag	Coverage Δ
#smoketests	`42.53% <0%> (-7.97%)`	⬇️
#unittests	`65.2% <0%> (+0.28%)`	⬆️

Impacted Files	Coverage Δ
nipype/algorithms/modelgen.py	`54.56% <0%> (-8.8%)`	⬇️
nipype/algorithms/rapidart.py	`35% <0%> (-29.42%)`	⬇️
nipype/interfaces/fsl/model.py	`55.26% <0%> (-25.35%)`	⬇️
nipype/interfaces/spm/base.py	`68.64% <0%> (-18.49%)`	⬇️
nipype/workflows/fmri/fsl/preprocess.py	`72.67% <0%> (-13.39%)`	⬇️
nipype/interfaces/fsl/preprocess.py	`72.7% <0%> (-9.91%)`	⬇️
nipype/pipeline/plugins/linear.py	`79.06% <0%> (-6.98%)`	⬇️
nipype/utils/subprocess.py	`87.31% <0%> (-6.72%)`	⬇️
nipype/interfaces/fsl/utils.py	`63.8% <0%> (-6.53%)`	⬇️
... and 25 more

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effigies

This looks reasonable. A few suggestions.

nipype/algorithms/modelgen.py

satra · 2019-02-14T16:41:24Z

just a note that we may have to do something different between SPM12 and prior versions.

in pre SPM12, orth was sequential and order mattered (and interpretation mattered). this was changed in SPM12, where you can orthgonalize things independently to the same variable, but i have not had a chance to play with this. perhaps @gllmflndn can also help us out :)

@hstojic - if you know how this is done, we should incorporate a version specific option.

effigies · 2019-02-20T14:08:39Z

@hstojic Just a heads up that we're going to try to release on Monday, so it'd be good to have any PRs ready by Friday if possible. (No big deal if we have to push off another month.)

I'll let this note stand in for #2857 and #2861 as well.

hstojic · 2019-02-21T08:19:31Z

just a note that we may have to do something different between SPM12 and prior versions.

in pre SPM12, orth was sequential and order mattered (and interpretation mattered). this was changed in SPM12, where you can orthgonalize things independently to the same variable, but i have not had a chance to play with this. perhaps @gllmflndn can also help us out :)

@hstojic - if you know how this is done, we should incorporate a version specific option.

Good catch. I don't know the SPM code well enough to try to create equivalent version for SPM8. For now i would simply condition this on SPM12, sounds good?

hstojic · 2019-02-21T12:25:12Z

I tried it out with SPM8, it fails in the estimation step but for some other reason related to the output (below). Design step goes fine, SPM8 simply ignores orth option in fmri_spec, so no need for any special treatment.

I updated the code with @effigies suggestions, pushing it shortly.

[Node] Error on "repsup_susan6_ydiff_test_l1_l1pipeline.analysis.estimate" (/media/hstojic/dataneuro/fnclearning_fmri/dProcessed/nipype_work/repsup_susan6_ydiff_test_l1_l1pipeline/analysis/_subject_s010/estimate)
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-5-27342c4bf114> in <module>()
     16     l1pipeline.run(
     17         'MultiProc',
---> 18         plugin_args = {'n_procs': pars['resources']['n_cores']}
     19     )
     20     l1pipeline._get_inputs()

/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.pyc in run(self, plugin, plugin_args, updatehash)
    593         if str2bool(self.config['execution']['create_report']):
    594             self._write_report_info(self.base_dir, self.name, execgraph)
--> 595         runner.run(execgraph, updatehash=updatehash, config=self.config)
    596         datestr = datetime.utcnow().strftime('%Y%m%dT%H%M%S')
    597         if str2bool(self.config['execution']['write_provenance']):

/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/plugins/base.pyc in run(self, graph, config, updatehash)
    160                         if result['traceback']:
    161                             notrun.append(
--> 162                                 self._clean_queue(jobid, graph, result=result))
    163                         else:
    164                             self._task_finished_cb(jobid)

/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/plugins/base.pyc in _clean_queue(self, jobid, graph, result)
    222 
    223         if str2bool(self._config['execution']['stop_on_first_crash']):
--> 224             raise RuntimeError("".join(result['traceback']))
    225         crashfile = self._report_crash(self.procs[jobid], result=result)
    226         if jobid in self.mapnodesubids:

RuntimeError: Traceback (most recent call last):
  File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 523, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 597, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/interfaces/spm/model.py", line 283, in _list_outputs
    outtype = 'nii' if '12' in self.version.split('.')[0] else 'img'
AttributeError: 'NoneType' object has no attribute 'split'

satra · 2019-02-21T12:27:05Z

@hstojic - that particular error is because for some reason it cannot determine spm version: self.version

satra · 2019-02-21T12:29:49Z

nipype/algorithms/modelgen.py

+       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.


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.

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

default == independent orthogonalization

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.

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

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

mgxd · 2019-03-27T17:56:02Z

hi @hstojic - is this ready for another review? anything I can do to help?

hstojic · 2019-03-28T08:19:19Z

To my understanding, @satra is trying to inquire with @gllmflndn about enabling it for SPM8.

Otherwise, I would be fine with the solution as is, we can simply state it will work only with SPM12 where that option exists.

effigies · 2019-09-05T02:34:24Z

@satra @gllmflndn Just a bump on this one. Any news?

carolfs · 2021-02-16T19:56:08Z

Is there any news on this pull request? I've been applying this patch to my nipype installation because this option is very useful.

YukunQu · 2022-01-25T08:38:00Z

I didn't find the change in last version nipype 1.7.0. Is it discarded or some bugs or another way to excute?

carolfs · 2022-07-07T17:58:49Z

This option is so useful. Hoping it will be added to nipype soon.

adding SPM orth argument to the SpecifyModel class

507aafc

effigies reviewed Feb 14, 2019

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effigies changed the title ~~ENH: adding SPM orth argument to the SpecifyModel class~~ ENH: Enable orthogonalization in SPM models via SpecifyModel Feb 14, 2019

effigies added this to the 1.1.9 milestone Feb 14, 2019

satra reviewed Feb 21, 2019

View reviewed changes

removed whitespaces, added ValueError if orth not None

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effigies mentioned this pull request Feb 22, 2019

REL: 1.1.9 #2884

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removed trailing whitespaces

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effigies modified the milestones: 1.1.9, 1.2.0 Feb 24, 2019

effigies modified the milestones: 1.2.0, 1.2.1 May 8, 2019

effigies modified the milestones: 1.2.1, 1.2.2 Aug 16, 2019

oesteban modified the milestones: 1.2.2, 1.3.0, 1.2.3 Sep 5, 2019

effigies modified the milestones: 1.2.3, future Sep 18, 2019

effigies added the blocked label Sep 18, 2019

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ENH: Enable orthogonalization in SPM models via SpecifyModel #2870

ENH: Enable orthogonalization in SPM models via SpecifyModel #2870

hstojic commented Jan 31, 2019

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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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hstojic commented Jan 31, 2019

Summary

Acknowledgment

codecov-io commented Feb 4, 2019

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