- stat on different SC vertebraes

- "process-data.sh" uses affine rescale

affine-rescale.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+# -*- coding: utf-8
+#########################################################################################
+#
+# Rescale image by changing subject image affine ndarray
+# 
+#
+# example: python csa_rescale_stat.py -i <results>
+# ---------------------------------------------------------------------------------------
+# Authors: Paul Bautin
+#
+# About the license: see the file LICENSE.TXT
+#########################################################################################
+import glob, os, sys
+from numpy.random import randn
+import numpy as np
+import argparse
+
+import nibabel as nib
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description='apply isotropic rescaling to image:',
+        add_help=None,
+        formatter_class=argparse.RawTextHelpFormatter,
+        prog=os.path.basename(__file__).strip(".py"))
+
+    mandatory = parser.add_argument_group("\nMANDATORY ARGUMENTS")
+    mandatory.add_argument(
+        "-i",
+        required=True,
+        help='path to T2w mri image',
+    )
+    mandatory.add_argument(
+        "-r",
+        required=True,
+        help='rescaling coefficient',
+    )
+    optional = parser.add_argument_group("\nOPTIONAL ARGUMENTS")
+    optional.add_argument(
+        '-h',
+        help='Help',
+        nargs="*"
+    )
+    return parser
+
+
+#MAIN
+############################################################
+def main(fname, coef_r):
+    print(coef_r)
+    # iterate transformation for each subject,
+    img = nib.load(fname) # load image
+    data = img.get_fdata()# load data
+    img.affine[:3,:3] = img.affine[:3,:3]*float(coef_r) # apply rescale
+    img_t = nib.Nifti1Image(data, img.affine) # changge affine for data
+
+    # save rescaled image
+    fname_out = fname.split('.nii.gz')[0] + '_r'+str(coef_r)+'.nii.gz'
+    nib.save(img_t, fname_out)
+
+#RUN
+############################################################
+if __name__ == "__main__":
+    # get parser elements
+    parser = get_parser()
+    arguments = parser.parse_args(args=None if sys.argv[0:] else ['--help'])
+    fname = arguments.i
+    coef_r = arguments.r
+    main(fname, coef_r)