Thanks to visit codestin.com
Credit goes to github.com

Skip to content

ENH Expand spm interface thresholding options #3333

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ldeangelisphys wants to merge 4 commits into
base: master
Choose a base branch
from
Open

ENH Expand spm interface thresholding options #3333

Changes from 1 commit
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
d78ba24
Allow for choosing between FDR, FWE and uncorrected threshold
May 3, 2021
662ec09
Add FWEc clustersize correction (use_topo_fwe) and turn off default u…
May 3, 2021
79285f7
Added my name in the .zenodo.json file
May 3, 2021
11f13ae
Merge branch 'master' into expand_spm_functionalities
ldeangelisphys May 4, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Next Next commit
Allow for choosing between FDR, FWE and uncorrected threshold 
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
  • Loading branch information
Lorenzo De Angelis committed May 3, 2021
commit d78ba2491ba3ceec391bcb5a067670db42b2fc2f
36 changes: 24 additions & 12 deletions nipype/interfaces/spm/model.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -522,13 +522,22 @@ class ThresholdInputSpec(SPMCommandInputSpec):
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(
Copy link
Member

@effigies effigies Oct 15, 2021

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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).

True,
# use_fwe_correction = traits.Bool(
# True,
# usedefault=True,
# desc=('whether to use FWE (Bonferroni) '
# 'correction for initial threshold '
# '(height_threshold_type has to be '
# 'set to p-value)'))
multitest_correction = traits.Enum(
'none',
'FWE',
'FDR',
usedefault=True,
desc=('whether to use FWE (Bonferroni) '
'correction for initial threshold '
'(height_threshold_type has to be '
'set to p-value)'))
desc=('Whether to use a correction '
'for multiple test. '
'Possible choices are FWE, FDR '
'or none'))
use_topo_fdr = traits.Bool(
True,
usedefault=True,
Expand Down Expand Up @@ -578,7 +587,6 @@ class Threshold(SPMCommand):

Examples
--------

>>> thresh = Threshold()
>>> thresh.inputs.spm_mat_file = 'SPM.mat'
>>> thresh.inputs.stat_image = 'spmT_0001.img'
Expand All @@ -600,11 +608,11 @@ def _gen_pre_topo_map_filename(self):
def _make_matlab_command(self, _):
script = "con_index = %d;\n" % self.inputs.contrast_index
script += "cluster_forming_thr = %f;\n" % self.inputs.height_threshold
if self.inputs.use_fwe_correction:
script += "thresDesc = 'FWE';\n"
else:
script += "thresDesc = 'none';\n"

script += "thresDesc = '%s';\n" % self.inputs.multitest_correction
# if self.inputs.use_fwe_correction:
# script += "thresDesc = 'FWE';\n"
# else:
# script += "thresDesc = 'none';\n"
if self.inputs.use_topo_fdr:
script += "use_topo_fdr = 1;\n"
else:
Expand All @@ -629,11 +637,15 @@ def _make_matlab_command(self, _):
R = SPM.xVol.R;
S = SPM.xVol.S;
n = 1;
VspmSv = cat(1,SPM.xCon(con_index).Vspm);

switch thresDesc
case 'FWE'
cluster_forming_thr = spm_uc(cluster_forming_thr,df,STAT,R,n,S);

case 'FDR'
cluster_forming_thr = spm_uc_FDR(cluster_forming_thr,df,STAT,n,VspmSv,0);

case 'none'
if strcmp(height_threshold_type, 'p-value')
cluster_forming_thr = spm_u(cluster_forming_thr^(1/n),df,STAT);
Expand Down