From 8eb9bfebeeb91bd22ceb8a1dcb15eeb434ed37b9 Mon Sep 17 00:00:00 2001
From: Jeff Stout <stoutjd@nih.gov>
Date: Tue, 6 Feb 2024 10:55:18 -0500
Subject: [PATCH] Helper script for plotting volumetric data to fsaverage
 surface

---
 cmdline/plot_vol2surf.py | 69 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100755 cmdline/plot_vol2surf.py

diff --git a/cmdline/plot_vol2surf.py b/cmdline/plot_vol2surf.py
new file mode 100755
index 0000000..271e2c1
--- /dev/null
+++ b/cmdline/plot_vol2surf.py
@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Feb  5 16:29:11 2024
+
+@author: jstout
+"""
+
+import nilearn
+from nilearn import datasets
+import numpy as np
+from nilearn import surface
+from nilearn import plotting
+from matplotlib.pyplot import subplots
+
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-threshold', default=0.1, type=float)
+    parser.add_argument('-group_nii',
+                          help='This is the group data that hase been volumetrically warped to fsaverage'
+                          )
+    args = parser.parse_args()
+    threshold = args.threshold
+    ave_fname = args.group_nii
+
+fsaverage = datasets.fetch_surf_fsaverage()
+curv_right = surface.load_surf_data(fsaverage.curv_right)
+curv_right_sign = np.sign(curv_right)
+
+curv_left = surface.load_surf_data(fsaverage.curv_left)
+curv_left_sign = np.sign(curv_left)
+
+texture_rh = surface.vol_to_surf(ave_fname, fsaverage.pial_right)
+texture_lh = surface.vol_to_surf(ave_fname, fsaverage.pial_left)
+
+
+
+fig, ax = subplots(2,2, subplot_kw={'projection': '3d'})
+
+## Lateral
+plotting.plot_surf_stat_map(
+    fsaverage.infl_left, texture_lh, hemi='left',
+    title='Surface left hemisphere', colorbar=True,
+    threshold=threshold, bg_map=curv_right_sign, axes=ax[0,0]
+)
+
+plotting.plot_surf_stat_map(
+    fsaverage.infl_right, texture_rh, hemi='right',
+    title='Surface right hemisphere', colorbar=True,
+    threshold=threshold, bg_map=curv_right_sign, axes=ax[0,1]
+)
+
+## Medial
+plotting.plot_surf_stat_map(
+    fsaverage.infl_left, texture_lh, hemi='left',
+    title='Surface left hemisphere', view='medial',colorbar=True,
+    threshold=threshold, bg_map=curv_right_sign, axes=ax[1,0]
+)
+
+plotting.plot_surf_stat_map(
+    fsaverage.infl_right, texture_rh, hemi='right',
+    title='Surface right hemisphere', view='medial', colorbar=True,
+    threshold=threshold, bg_map=curv_right_sign, axes=ax[1,1]
+)
+
+fig.show()
+_ = input('Enter anything to close the plot')