ENH Expand spm interface thresholding options #3333
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
reviewed
Oct 15, 2021
| @@ -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( | |||
There was a problem hiding this comment.
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).
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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)
Acknowledgment