dgobbi · December 13, 2023 17:36 · Dec 13, 2023
diff --git a/split_nifti.py b/split_nifti.py
@@ -0,0 +1,105 @@
+#! /usr/bin/env python
+
+"""
+Split a 4D NIFTI file into separate volumes.
+
+Dec 11, 2023
+David Gobbi
+"""
+
+usage="""
+usage: split_nifti file.nii.gz
+
+If the file has more than 3 dimensions, then it will be split into
+separate volumes.  For example, if there are 2 volumes, the output is:
+
+    file-vol1.nii.gz
+    file-vol2.nii.gz
+
+If "file.bval" exists in the same directory (e.g. from dcm2niix), then
+the bvals will be used to name the output:
+
+    file-vol1-b1000.nii.gz
+    file-vol2-b1000.nii.gz
+    file-vol3-b0.nii.gz
+
+The ordering will match the ordering in the .bval file.
+"""
+
+import argparse
+import gzip
+import struct
+import sys
+import os
+import os.path
+
+def split_nifti(filename):
+    """Split a NIFTI file into -vol1, -vol2, etc.
+    If there is a bval, then add include -b<bval>.
+    """
+    # length of NIFTI header
+    header_size = 348
+    if filename.endswith(".nii.gz"):
+        file = gzip.open(filename, 'rb')
+        basename = filename[0:-7]
+    elif filename.endswith(".nii"):
+        file = open(filename, 'rb')
+        basename = filename[0:-4]
+    else:
+        sys.stderr.write("File doesn't appear to be NIFTI: %s\n" % (filename))
+
+    header = file.read(header_size)
+    size_check = struct.unpack('i', header[0:4])[0]
+    if size_check != header_size:
+        sys.stderr.write("File doesn't appear to be NIFTI: %s\n" % (filename))
+        return None
+
+    # get the dims and pixdims
+    dims = struct.unpack('h'*8, header[40:56])
+    pixdim = struct.unpack('f'*8, header[76:108])
+    vox_offset = int(struct.unpack('f', header[108:112])[0])
+    nvol = 1
+    for i in dims[4:1+dims[0]]:
+        nvol = nvol * i
+    pad  = file.read(vox_offset - header_size)
+
+    if nvol == 1:
+        file.close()
+        return
+
+    image = file.read()
+    file.close()
+
+    volsize = int(len(image)/nvol)
+    newheader = header[:40] + struct.pack('h'*8, 3, dims[1], dims[2], dims[3], 1, 1, 1, 1) + header[56:]
+
+    bvals = []
+    bvalfile = basename + ".bval"
+    if os.path.exists(bvalfile):
+        file = open(bvalfile, 'r')
+        t = file.read()
+        file.close()
+        bvals = [float(x) for x in t.split()]
+
+    for i in range(nvol):
+        if len(bvals) == nvol:
+            btext = "-b%g" % bvals[i]
+        else:
+            btext = ""
+        fname = "%s-vol%d%s.nii.gz" % (basename, i+1, btext)
+        if os.path.exists(fname):
+            continue
+        file = gzip.open(fname, 'wb')
+        file.write(newheader)
+        file.write(pad)
+        file.write(image[volsize*i:volsize*(i+1)])
+        file.close()
+
+if __name__ == '__main__':
+
+    if len(sys.argv) < 2 or sys.argv[1].startswith('-') or not os.path.exists(sys.argv[1]):
+        print(usage)
+        sys.exit(0)
+
+    filename = sys.argv[1]
+    split_nifti(filename)