\(\newcommand{L}[1]{\| #1 \|}\newcommand{VL}[1]{\L{ \vec{#1} }}\newcommand{R}[1]{\operatorname{Re}\,(#1)}\newcommand{I}[1]{\operatorname{Im}\, (#1)}\)
Sometimes, the NIfTI image stores the TR in the headerΒΆ
>>> import numpy as np
>>> # print arrays to 4 decimal places
>>> np.set_printoptions(precision=4, suppress=True)
>>> import nibabel as nib
The NIfTI1 standard suggests putting the TR of a functional image, into the voxel dimension field of the header.
You can get the voxel (plus TR) dimensions with the get_zooms method of
the header object:
>>> func_img = nib.load('ds114_sub009_t2r1.nii')
>>> header = func_img.header
>>> header.get_zooms()
(4.0, 4.0, 4.0000162, 2.5)
In this case, the image spatial voxel sizes are (4 by 4 by 4) millimeters, and the TR is 2.5 seconds.
In fact these values come from the NIfTI header field called pixdim:
>>> print(header)
<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
sizeof_hdr : 348
data_type : b''
db_name : b'?TR:2500.000 TE:50'
extents : 0
session_error : 0
regular : b'r'
dim_info : 0
dim : [ 4 64 64 30 173 1 1 1]
intent_p1 : 0.0
intent_p2 : 0.0
intent_p3 : 0.0
intent_code : none
datatype : int16
bitpix : 16
slice_start : 0
pixdim : [-1. 4. 4. 4. 2.5 1. 1. 1. ]
vox_offset : 0.0
scl_slope : nan
scl_inter : nan
slice_end : 0
slice_code : unknown
xyzt_units : 10
cal_max : 0.0
cal_min : 0.0
slice_duration : 0.0
toffset : 0.0
glmax : 255
glmin : 0
descrip : b''
aux_file : b''
qform_code : scanner
sform_code : scanner
quatern_b : 0.0
quatern_c : 0.9958999752998352
quatern_d : -0.090460866689682
qoffset_x : 124.24400329589844
qoffset_y : -103.4496841430664
qoffset_z : -33.49285888671875
srow_x : [ -4. 0. 0. 124.244]
srow_y : [ 0. 3.9345 0.7207 -103.4497]
srow_z : [ 0. -0.7207 3.9346 -33.4929]
intent_name : b''
magic : b'n+1'
Unfortunately, it is common for people writing NIfTI images not to write this information correctly into the header, so we have to be careful, and very suspicious, if the TR value appears to be 0 or 1.