--- a
+++ b/utils/resizeScans.py
@@ -0,0 +1,124 @@
+import os
+import numpy as np
+import nibabel as nib
+import time
+import math
+import random
+import glob
+import collections
+import sys
+import random
+from random import randint
+import time
+import datetime
+import subprocess
+from docopt import docopt
+import PP
+import normalizations as NORM
+import augmentations as AUGM
+#this utility resizes images to a specific dimension given by the user
+#NOTE: this does not register the images to a template, only resizes them
+
+#pass flair folder
+#will find and resize the rest .. for wmh, ../gifs for gifs
+
+docstr = """Write something here
+
+Usage: 
+    resizeScans.py [options]
+
+Options:
+    -h, --help                  Print this message
+    --mainFolderPath=<str>      Main folder path [default: ../../Data/MS2017b/]
+    --FLAIR_name=<str>          FLAIR prefix [default: FLAIR.nii.gz]
+    --WMH_name=<str>            WMH prefix [default: wmh.nii.gz]
+    --GIF_name=<str>            GIF prefix [default: parcellation.nii.gz]
+    --CIRC_name=<str>           CIRC prefix [default: circumference.nii.gz]
+    --gpu0=<int>                GPU number [default: 0]
+    --useGPU=<int>              Use GPU [default: 0]
+    --size=<str>                Shape to resize to [default: 200x200x100]
+    --noGIFS                    Dont Resize GIFS
+    --postfix=<str>             Postfix name to add [default: _200x200x100orig]
+    --withNorm=<int>            Include normalization [default: 1]
+"""
+
+
+args = docopt(docstr, version='v0.1')
+#resize256x256x256
+noGIFS = args['--noGIFS']
+main_folder_path = args['--mainFolderPath']
+
+FLAIR_name = args['--FLAIR_name']
+WMH_name = args['--WMH_name']
+GIF_name = args['--GIF_name']
+CIRC_name = args['--CIRC_name']
+postfix = args['--postfix']
+norm_type = ['hist', 'insubjectvar']
+with_norm = int(args['--withNorm'])
+glob_folders = glob.glob(main_folder_path + 'scans/*')
+
+new_size = args['--size'].split('x')
+new_size = np.array([int(i) for i in new_size])
+
+
+def convertSize(from_path, to_path, new_size, interpolation = 'interpolate'):
+	img = PP.numpyFromScan(from_path)
+	shape = img.shape
+	r1 = shape[0] / float(new_size[0])
+	r2 = shape[1] / float(new_size[1])
+	r3 = shape[2] / float(new_size[2])
+	command = "mri_convert " + from_path + " " + to_path + " -ds " + str(r1) + " " + str(r2) + " " + str(r3) + " -rt " + interpolation
+	print(command)
+	#normalize
+	process = subprocess.Popen(command.split(), stdout=subprocess.PIPE)
+	process.communicate()
+
+def convertSize2(from_path, to_path, new_size, interpolation = 'interpolate'):
+	if interpolation == 'interpolate':
+		spline_order = [2]
+	elif interpolation == 'nearest':
+		spline_order = [0]
+
+	img_np, affine = PP.numpyFromScan(from_path, get_affine = True)
+	shape = img_np.shape
+	new_affine = np.copy(affine)
+	r1 = float(new_size[0]) / shape[0]
+	r2 = float(new_size[1]) / shape[1] 
+	r3 = float(new_size[2]) / shape[2] 
+	new_affine[:,0] /= r1
+	new_affine[:,1] /= r2
+	new_affine[:,2] /= r3
+
+	img_np = AUGM.applyScale([img_np], [r1,r2,r3], spline_order)[0].squeeze()
+
+	PP.saveScan(img_np, new_affine, to_path)
+	return new_affine
+
+def normalizeScan(from_path, to_path, main_folder_path = main_folder_path):
+	img_np, affine = PP.numpyFromScan(from_path, get_affine = True)
+	img_np = NORM.applyNormalize(img_np.squeeze(), postfix, norm_method = norm_type[0], main_folder_path = main_folder_path)
+	img_np = NORM.applyNormalize(img_np.squeeze(), postfix, norm_method = norm_type[1], main_folder_path = main_folder_path)
+	PP.saveScan(img_np, affine, to_path)
+
+if __name__ == "__main__":
+
+	for scan_folder in glob_folders:
+		folder_num = os.path.basename(scan_folder)
+
+		flair_path = os.path.join(main_folder_path, 'scans', folder_num, 'pre', FLAIR_name)
+		wmh_path = os.path.join(main_folder_path, 'scans', folder_num, WMH_name)
+		gif_path = os.path.join(main_folder_path, 'gifs', folder_num, GIF_name)
+		circ_path = os.path.join(main_folder_path, 'gifs', folder_num, CIRC_name)
+
+		to_flair_path = flair_path.replace('.nii.gz', postfix + '.nii.gz')
+		to_wmh_path = wmh_path.replace('.nii.gz', postfix + '.nii.gz')
+		to_gif_path = gif_path.replace('.nii.gz', postfix + '.nii.gz')
+		to_circ_path = circ_path.replace('.nii.gz', postfix + '.nii.gz')
+
+		convertSize2(flair_path, to_flair_path, new_size)
+		if with_norm:
+			normalizeScan(to_flair_path, to_flair_path)
+
+		convertSize2(wmh_path, to_wmh_path, new_size, 'nearest')
+		if not noGIFS:
+			convertSize2(gif_path, to_gif_path, new_size, 'nearest')
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