fisherz

scripts/fisher_z.py

@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+#
+# Convert XCP_D Pearson output to Fisher Z
+
+import argparse
+import bids
+import numpy
+import os
+import pandas
+import sys
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--xcpd_dir', required=True, 
+    help='Absolute path of xcpd output (must match subject/session/etc of fmriprep)')
+args = parser.parse_args()
+
+# Parse BIDS structure
+bids_xcpd = bids.layout.BIDSLayout(args.xcpd_dir, validate=False)
+
+# Doesn't work - uniqueness conflict in datatype
+#bids_xcpd = bids.layout.BIDSLayout(args.xcpd_dir, validate=False, config=['bids', 'xcp_d_bids_config.json'])
+
+# Doesn't work - deprecated, and still doesn't grab stat or seg
+#bids_xcpd = bids.layout.BIDSLayout(args.xcpd_dir, validate=False, config_filename='xcp_d_bids_config.json')
+
+# Hack is to just get filename, replace pearsoncorrelation with fisherz, and be done
+
+# Get all correlation files
+
+# Get corresponding number of time points
+
+# Load R, convert, save
+
+
+
+# Find input files
+
+corr_tsvs_all = bids_xcpd.get(
+    extension='.tsv',
+    suffix='relmat',
+    )
+
+# Stat is not a valid entity by default. It is defined here
+# https://github.com/PennLINC/xcp_d/blob/main/xcp_d/data/xcp_d_bids_config.json
+# But I don't know how to use that. So just manually reduce to list to only 
+# pearsoncorrelation here
+corr_tsvs = [x for x in corr_tsvs_all if x.endswith('stat-pearsoncorrelation_relmat.tsv')]
+
+# Process them
+for corr_tsv in corr_tsvs:
+
+    # Create filenames
+    fname = os.path.join(corr_tsv.dirname, corr_tsv.filename)
+    timeseries_tsv = fname.replace('stat-pearsoncorrelation_relmat.tsv', 'stat-mean_timeseries.tsv')
+    fisherz_tsv = fname.replace('stat-pearsoncorrelation_relmat.tsv', 'stat-fisherz_relmat.tsv')
+
+    # Get the timeseries and compute DOF
+    timeseries = pandas.read_csv(timeseries_tsv, sep='\t')
+    ntimepoints = timeseries.shape[0]
+
+    # Compute Fisher Z from R and save to file
+    pearsonr = pandas.read_csv(corr_tsv, sep='\t', index_col=0)
+    fisherz = numpy.arctanh(pearsonr) * numpy.sqrt(ntimepoints - 3)
+    fisherz.to_csv(fisherz_tsv, sep='\t')