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[ENH] Enable SPM voxel-based FDR #3558

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Merged
merged 2 commits into from
May 17, 2023
Merged

[ENH] Enable SPM voxel-based FDR #3558

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73d6084
added voxel-based FDR thresholding in SPM
mmbannert Apr 3, 2023
27fc828
added voxel-based FDR thresholding in SPM
mmbannert Apr 3, 2023
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
5 changes: 5 additions & 0 deletions .zenodo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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": [
Expand Down
25 changes: 24 additions & 1 deletion nipype/interfaces/spm/model.py
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Expand Up @@ -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,
Expand Down Expand Up @@ -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"

Expand All @@ -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;
Expand All @@ -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);
Expand Down