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ENH Expand spm interface thresholding options #3333

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Summary

I added the option of using FDR correction (at the voxel level) and the option to choose between FWEc and FDRc for the clustersize correction (only FDRc was present through use_topo_fdr) to the SPM interface

Fixes # .

List of changes proposed in this PR (pull-request)

  • Added FDR correction
  • added option for both FDRc and FWEc clustersize correction
  • include FDRc and FWEc cluster threshold in the output

Acknowledgment

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

Lorenzo De Angelis added 3 commits May 3, 2021 10:53
The variable use_fwe_correction has been replaced with a multitest_correction
variable which can be equal to 'none' for uncorrected threshold,
'FWE' for FWE correction adn 'FDR' for FDR correction
…se_topo_fdr

Now there is another varialbe called use_topo_fwe that uses FWEc cluster size
correction. Additionally, both FWEc and FDRc are returned to the user as output.
@effigies effigies mentioned this pull request Oct 15, 2021
15 tasks
@@ -574,23 +574,26 @@ class ThresholdInputSpec(SPMCommandInputSpec):
)
stat_image = File(exists=True, desc="stat image", copyfile=False, mandatory=True)
contrast_index = traits.Int(
mandatory=True, desc="which contrast in the SPM.mat to use"
)
use_fwe_correction = traits.Bool(
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We have to keep the old options around so that we don't break existing workflows. You can deprecate it though (see https://nipype.readthedocs.io/en/latest/devel/interface_specs.html).

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2 participants