Upload New File

OB_pipeline/cmore_segSize.py

+#!/usr/bin/env python
+
+# Author: Christoph Arthofer
+# Copyright: FMRIB 2021
+
+import nibabel as nib
+import numpy as np
+import pandas as pd
+
+id_paths = ['IDs.txt']
+label_path_temp = "/path/to/labels/OB_labels_to_%s.nii.gz"
+
+vols = []
+ids = []
+tbvs = []
+for id_path in id_paths:
+    df_ids = pd.read_csv(id_path, header=None, names=['subject_ID'], dtype={'subject_ID':str})
+    ls_ids = df_ids['subject_ID'].tolist()
+
+    for id in ls_ids:
+        img_path = label_path_temp % id
+        label_nib = nib.load(img_path)
+        header = label_nib.header
+        label_arr = label_nib.get_fdata()
+        mask_count = np.sum(label_arr)
+        vol = mask_count * np.prod(header['pixdim'][1:4])
+        print('id:', id, ' pixdim:', header['pixdim'], ' volume:', vol)
+        vols.append(vol)
+        ids.append(id)
+
+ob_vols = {'vol':vols}
+df = pd.DataFrame(data=ob_vols,index=ids)
+print(df)
+df.to_csv('/path/to/volume/measurement-output/OB_volumes.csv',header=True)