[ENH] Enable SPM voxel-based FDR

.pre-commit-config.yaml

@@ -2,13 +2,13 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v3.4.0
+ rev: v4.4.0
  hooks:
  - id: trailing-whitespace
  - id: end-of-file-fixer
  - id: check-yaml
  - id: check-added-large-files
 - repo: https://github.com/psf/black
- rev: 20.8b1
+ rev: 23.3.0
  hooks:
  - id: black

.zenodo.json

@@ -890,6 +890,11 @@
  "affiliation": "MIT, HMS",
  "name": "Ghosh, Satrajit",
  "orcid": "0000-0002-5312-6729"
+ },
+ {
+ "affiliation": "University of Tübingen and MPI for Biological Cybernertics",
+ "name": "Bannert, Michael M.",
+ "orcid": "0000-0003-1010-7517"
  }
  ],
  "keywords": [

nipype/interfaces/spm/model.py

@@ -586,6 +586,16 @@ class ThresholdInputSpec(SPMCommandInputSpec):
  "set to p-value)"
  ),
  )
+ use_vox_fdr_correction = traits.Bool(
+ False,
+ usedefault=True,
+ desc=(
+ "whether to use voxel-based FDR "
+ "correction for initial threshold "
+ "(height_threshold_type has to be "
+ "set to q-value)"
+ ),
+ )
  use_topo_fdr = traits.Bool(
  True,
  usedefault=True,
@@ -661,8 +671,16 @@ 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:
+
+ if self.inputs.use_fwe_correction and self.inputs.use_vox_fdr_correction:
+ raise ValueError(
+ "'use_fwe_correction' and 'use_vox_fdr_correction' can't both be True"
+ )
+
+ if self.inputs.use_fwe_correction and not self.inputs.use_vox_fdr_correction:
  script += "thresDesc = 'FWE';\n"
+ elif self.inputs.use_vox_fdr_correction and not self.inputs.use_fwe_correction:
+ script += "thresDesc = 'FDR';\n"
  else:
  script += "thresDesc = 'none';\n"
 
@@ -687,6 +705,8 @@ def _make_matlab_command(self, _):
 FWHM = SPM.xVol.FWHM;
 df = [SPM.xCon(con_index).eidf SPM.xX.erdf];
 STAT = SPM.xCon(con_index).STAT;
+VspmSv = cat(1,SPM.xCon(con_index).Vspm);
+
 R = SPM.xVol.R;
 S = SPM.xVol.S;
 n = 1;
@@ -695,6 +715,9 @@ def _make_matlab_command(self, _):
  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);